Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate NmrBucketing_script.R @ 4:d61f6ceef5d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
author lecorguille
date Tue, 22 Nov 2016 05:22:03 -0500
parents 58679e85745f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
1 ################################################################################################
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
2 # SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
3 # User : Galaxy #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
4 # Original data : -- #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
5 # Starting date : 20-10-2014 #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
6 # Version 1 : 18-12-2014 #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
7 # Version 2 : 07-01-2015 #
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
8 # Version 3 : 24-10-2016 #
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
9 # #
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
10 # Input files : modification on october 2016 #
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
11 # - Raw bruker files included in user-defined fileName #
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
12 # - Preprocessed files (alignment, ...) included in p x n dataframe #
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
13 ################################################################################################
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
14 NmrBucketing <- function(fileType,fileName,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
15 exclusionZonesBorders=NULL,graph=c("None","Overlay","One_per_individual"),
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
16 nomFichier,savLog.txtC = NULL)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
17 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
18 ## Option
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
19 ##---------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
20 strAsFacL <- options()$stringsAsFactors
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
21 options(stingsAsFactors = FALSE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
22 options(warn = -1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
23
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
24
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
25 ## Constants
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
26 ##---------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
27 topEnvC <- environment()
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
28 flgC <- "\n"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
29
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
30 ## Log file (in case of integration into Galaxy)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
31 ##----------------------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
32 if(!is.null(savLog.txtC))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
33 sink(savLog.txtC, append = TRUE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
34
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
35 ## Functions definition
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
36 ##---------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
37 ## RAW BRUKER FILE READING FUNCTION
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
38 NmRBrucker_read <- function(DataDir,SampleSpectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
39 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
40
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
41 bruker.get_param <- function (ACQ,paramStr)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
42 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
43 regexpStr <- paste("^...",paramStr,"=",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
44 as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
45 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
46
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
47 ACQFILE <- "acqus"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
48 SPECFILE <- paste(DataDir,"/1r",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
49 PROCFILE <- paste(DataDir,"/procs",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
50
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
51 ACQ <- readLines(ACQFILE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
52 TD <- bruker.get_param(ACQ,"TD")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
53 SW <- bruker.get_param(ACQ,"SW")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
54 SWH <- bruker.get_param(ACQ,"SW_h")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
55 DTYPA <- bruker.get_param(ACQ,"DTYPA")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
56 BYTORDA <- bruker.get_param(ACQ,"BYTORDA")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
57 #ENDIAN = ifelse( BYTORDA==0, "little", "big")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
58 ENDIAN <- "little"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
59 SIZE = ifelse( DTYPA==0, 4, 8)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
60
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
61 PROC <- readLines(PROCFILE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
62 OFFSET <- bruker.get_param(PROC,"OFFSET")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
63 SI <- bruker.get_param(PROC,"SI")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
64
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
65 to.read = file(SPECFILE,"rb")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
66 maxTDSI = max(TD,SI)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
67 # signal<-rev(readBin(to.read, what="int",size=SIZE, n=TD, signed = TRUE, endian = ENDIAN))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
68 signal<-rev(readBin(to.read, what="int",size=SIZE, n=maxTDSI, signed = TRUE, endian = ENDIAN))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
69 close(to.read)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
70
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
71 td <- length(signal)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
72
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
73 # dppm <- SW/(TD-1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
74 dppm <- SW/(td-1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
75 pmax <- OFFSET
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
76 pmin <- OFFSET - SW
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
77 ppmseq <- seq(from=pmin, to=pmax, by=dppm)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
78 signal <- 100*signal/max(signal)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
79
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
80 SampleSpectrum <- cbind(ppmseq,signal)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
81 return(SampleSpectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
82 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
83
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
84 ## SPECTRUM BUCKETING
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
85 NmrBrucker_bucket <- function(spectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
86 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
87 # Initialisations
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
88 b <- 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
89 j <- 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
90 # Variable number
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
91 J <- round((spectrum[1,1]-spectrum[dim(spectrum)[1],1])/bucketSize)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
92 f.bucket <- matrix(rep(0,J*2),ncol=2)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
93 colnames(f.bucket) <- c("Bucket",FileNames[i])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
94
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
95
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
96 # Data bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
97 while (j < dim(spectrum)[1])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
98 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
99 # chemical shift
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
100 BUB <- spectrum[j,1]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
101
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
102 # In zone exclusion?
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
103 exclusion.in <- FALSE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
104 if (!is.null(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
105 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
106 for (k in 1:nrow(exclusion.zone.m))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
107 if (BUB <= exclusion.zone.m[k,1] && exclusion.zone.m[k,2] < BUB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
108 exclusion.in <- TRUE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
109 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
110
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
111 if (exclusion.in)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
112 j <- j + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
113
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
114 if (!exclusion.in)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
115 # Bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
116 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
117 BLB <- BUB - bucketSize
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
118 bucket <- spectrum[j,]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
119 while (j < dim(spectrum)[1] && spectrum[j,1] > BLB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
120 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
121 j <- j + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
122 if (spectrum[j,1] > BLB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
123 bucket <- rbind(bucket,spectrum[j,])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
124 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
125
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
126 # Integration (trapezoid method)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
127 s <- cumtrapz(bucket[,1],bucket[,2])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
128 f.bucket[b,] <- c(round(mean(bucket[,1]),3),abs(s[length(s)][[1]]))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
129
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
130 # Next bucket boundary
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
131 BUB <- spectrum[j,1]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
132 b <- b + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
133 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
134 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
135 return(f.bucket)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
136 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
137
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
138 # Exclusion zones
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
139 if (!is.null(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
140 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
141 exclusion.zone.m <- matrix(exclusionZonesBorders[[1]],nrow=1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
142 if (length(exclusionZonesBorders) > 1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
143 for (k in 2:length(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
144 exclusion.zone.m <- rbind(exclusion.zone.m,exclusionZonesBorders[[k]])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
145 }
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
146
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
147 ## CHANGES
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
148 ## Inputs from zip or library (raw files)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
149 if (fileType == "zip")
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
150 {
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
151 # File names
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
152 FileNames <- list.files(fileName)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
153 n <- length(FileNames)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
154
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
155 # Reading and Bucketing
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
156 fileName <- paste(fileName,"/",sep="")
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
157
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
158 i <- 1
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
159 while (i <= n)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
160 {
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
161 # File reading
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
162 SampleDir <- paste(fileName,FileNames[i],"/1/",sep="")
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
163 setwd(SampleDir)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
164 DataDir <- "pdata/1"
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
165
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
166 rawSpectrum <- NmRBrucker_read(DataDir,rawSpectrum)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
167
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
168 orderedSpectrum <- rawSpectrum[order(rawSpectrum[,1],decreasing=T), ]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
169
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
170 # Removal of chemical shifts > leftBorder or < rightBorder boundaries
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
171 truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
172 truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
173
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
174 # Bucketing
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
175 spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
176
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
177 # spectrum Concatenation
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
178 if (i == 1)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
179 bucketedSpectra <- spectrum.bucket
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
180 if (i > 1)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
181 bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
182 colnames(bucketedSpectra)[i+1] <- FileNames[i]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
183
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
184 # Next sample
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
185 rm(spectrum.bucket)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
186 i <- i +1
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
187 }
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
188 # Directory
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
189 cd(fileName)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
190 }
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
191
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
192 ## Inputs from dataset (preprocessed files)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
193 if (fileType=="tsv")
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
194 {
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
195 FileNames <- colnames(fileName)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
196 n <- length(FileNames)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
197
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
198 for (i in 1:ncol(fileName))
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
199 {
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
200 orderedSpectrum <- cbind(as.numeric(rownames(fileName)),fileName[,i])
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
201 orderedSpectrum <- orderedSpectrum[order(orderedSpectrum[,1],decreasing=T), ]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
202
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
203 truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
204 truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
205
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
206 # Bucketing
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
207 spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
208
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
209 # spectrum Concatenation
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
210 if (i == 1)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
211 bucketedSpectra <- spectrum.bucket
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
212 if (i > 1)
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
213 bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
214 colnames(bucketedSpectra)[i+1] <- colnames(fileName)[i]
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
215 }
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
216 }
4
d61f6ceef5d6 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
lecorguille
parents: 3
diff changeset
217
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
218 identifiants <- gsub("([- , * { } | \\[ ])","_",colnames(bucketedSpectra)[-1])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
219 colnames(bucketedSpectra) <- c(colnames(bucketedSpectra)[1],identifiants)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
220
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
221 bucketedSpectra <- bucketedSpectra[bucketedSpectra[,1]!=0,]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
222 rownames(bucketedSpectra) <- paste("B",bucketedSpectra[,1],sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
223 bucketedSpectra <- bucketedSpectra[,-1]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
224
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
225 # Metadata matrice outputs
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
226 sampleMetadata <- data.frame(1:n)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
227 rownames(sampleMetadata) <- colnames(bucketedSpectra)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
228 colnames(sampleMetadata) <- "SampleOrder"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
229
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
230 variableMetadata <- data.frame(1:nrow(bucketedSpectra))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
231 rownames(variableMetadata) <- rownames(bucketedSpectra)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
232 colnames(variableMetadata) <- "VariableOrder"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
233
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
234 # Bucketed spectra graph
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
235 if (graph != "None")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
236 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
237 # Graphic Device opening
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
238 pdf(nomFichier,onefile=TRUE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
239
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
240 if (graph == "Overlay")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
241 {
3
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
242 x <- 1:length(bucketedSpectra[,1])
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
243 ymax <- max(bucketedSpectra)
3
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
244 plot(x,bucketedSpectra[,1],ylim=c(0,ymax),type='l',col=1,xlab="",xaxt="n",ylab="Intensity")
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
245 # x-axis labels
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
246 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
247 for (i in 2:ncol(bucketedSpectra))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
248 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
249 spectre <- bucketedSpectra[,i]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
250 lines(spectre,col=i)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
251 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
252 # legend(0,ymax,lty=c(1,1),legend=colnames(bucketedSpectra),col=1:ncol(bucketedSpectra))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
253 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
254 else
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
255 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
256 for (i in 1:ncol(bucketedSpectra))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
257 {
3
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
258 x <- 1:length(bucketedSpectra[,1])
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
259 plot(x,bucketedSpectra[,i],type='l',col=1,xlab="",xaxt="n",ylab="Intensity")
58679e85745f planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
lecorguille
parents: 2
diff changeset
260 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
261 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
262 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
263 dev.off()
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
264 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
265 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
266 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
267
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
268
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
269 #################################################################################################################
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
270 ## Typical function call
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
271 #################################################################################################################
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
272 ## StudyDir <- "K:/PROJETS/Metabohub/Bruker/Tlse_BPASourisCerveau/"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
273 ## upper <- 9.5
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
274 ## lower <- 0.8
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
275 ## bucket.width <- 0.01
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
276 ## exclusion <- TRUE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
277 ## exclusion.zone <- list(c(5.1,4.5))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
278 ## graphique <- "Overlay"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
279 ## nomFichier <- "Tlse_BPASourisCerveau_NmrBucketing_graph.pdf"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
280 ## tlse_cerveaupnd21.bucket <- NmrBucketing(StudyDir,upper,lower,bucket.width,exclusion,exclusion.zone,graphique,nomFichier)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
281 ## write.table(tlse_cerveaupnd21.bucket,file=paste(StudyDir,"Tlse_BPASourisCerveau_NmrBucketing_dataMatrix.tsv",sep=""),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
282 ## quote=FALSE,row.nmaes=FALSE,sep="\t")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
283 #################################################################################################################