Mercurial > repos > melpetera > batchcorrection

comparison easyrlibrary-lib/RcheckLibrary.R @ 0:71d83d8920bf draft

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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
author melpetera
date Tue, 09 Aug 2016 06:47:41 -0400
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-1:000000000000 0:71d83d8920bf
1 ######################################################
2 # R check library
3 # Coded by: M.Petera,
4 # - -
5 # R functions to use in R scripts
6 # (management of various generic subroutines)
7 # - -
8 # V0: script structure + first functions
9 # V1: More detailed error messages in match functions
10 ######################################################
11
12
13 # Generic function to return an error if problems have been encountered - - - -
14
15 check.err <- function(err.stock){
16
17 # err.stock = vector of results returned by check functions
18
19 if(length(err.stock)!=0){ stop("\n- - - - - - - - -\n",err.stock,"\n- - - - - - - - -\n") }
20
21 }
22
23
24
25
26 # Table match check functions - - - - - - - - - - - - - - - - - - - - - - - - -
27
28 # To check if dataMatrix and (variable or sample)Metadata match regarding identifiers
29 match2 <- function(dataMatrix, Metadata, Mtype){
30
31 # dataMatrix = data.frame containing dataMatrix
32 # Metadata = data.frame containing sampleMetadata or variableMetadata
33 # Mtype = "sample" or "variable" depending on Metadata content
34
35 err.stock <- NULL # error vector
36
37 id2 <- Metadata[,1]
38 if(Mtype=="sample"){ id1 <- colnames(dataMatrix)[-1] }
39 if(Mtype=="variable"){ id1 <- dataMatrix[,1] }
40
41 if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
42 err.stock <- c("\nData matrix and ",Mtype," metadata do not match regarding ",Mtype," identifiers.")
43 if(length(which(id1%in%id2))!=length(id1)){
44 if(length(which(!(id1%in%id2)))<4){ err.stock <- c(err.stock,"\n The ")
45 }else{ err.stock <- c(err.stock,"\n For example, the ") }
46 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
47 " do not appear in the ",Mtype," metadata file:\n")
48 identif <- id1[which(!(id1%in%id2))][1:min(3,length(which(!(id1%in%id2))))]
49 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
50 }
51 if(length(which(id2%in%id1))!=length(id2)){
52 if(length(which(!(id2%in%id1)))<4){ err.stock <- c(err.stock,"\n The ")
53 }else{ err.stock <- c(err.stock,"\n For example, the ") }
54 err.stock <- c(err.stock,"following identifiers found in the ",Mtype," metadata file\n",
55 " do not appear in the data matrix:\n")
56 identif <- id2[which(!(id2%in%id1))][1:min(3,length(which(!(id2%in%id1))))]
57 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
58 }
59 err.stock <- c(err.stock,"\nPlease check your data.\n")
60 }
61
62 return(err.stock)
63
64 }
65
66 # To check if the 3 standard tables match regarding identifiers
67 match3 <- function(dataMatrix, sampleMetadata, variableMetadata){
68
69 # dataMatrix = data.frame containing dataMatrix
70 # sampleMetadata = data.frame containing sampleMetadata
71 # variableMetadata = data.frame containing variableMetadata
72
73 err.stock <- NULL # error vector
74
75 id1 <- colnames(dataMatrix)[-1]
76 id2 <- sampleMetadata[,1]
77 id3 <- dataMatrix[,1]
78 id4 <- variableMetadata[,1]
79
80 if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
81 err.stock <- c(err.stock,"\nData matrix and sample metadata do not match regarding sample identifiers.")
82 if(length(which(id1%in%id2))!=length(id1)){
83 if(length(which(!(id1%in%id2)))<4){ err.stock <- c(err.stock,"\n The ")
84 }else{ err.stock <- c(err.stock,"\n For example, the ") }
85 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
86 " do not appear in the sample metadata file:\n")
87 identif <- id1[which(!(id1%in%id2))][1:min(3,length(which(!(id1%in%id2))))]
88 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
89 }
90 if(length(which(id2%in%id1))!=length(id2)){
91 if(length(which(!(id2%in%id1)))<4){ err.stock <- c(err.stock,"\n The ")
92 }else{ err.stock <- c(err.stock,"\n For example, the ") }
93 err.stock <- c(err.stock,"following identifiers found in the sample metadata file\n",
94 " do not appear in the data matrix:\n")
95 identif <- id2[which(!(id2%in%id1))][1:min(3,length(which(!(id2%in%id1))))]
96 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
97 }
98 }
99
100 if( length(which(id3%in%id4))!=length(id3) || length(which(id4%in%id3))!=length(id4) ){
101 err.stock <- c(err.stock,"\nData matrix and variable metadata do not match regarding variable identifiers.")
102 if(length(which(id3%in%id4))!=length(id3)){
103 if(length(which(!(id3%in%id4)))<4){ err.stock <- c(err.stock,"\n The ")
104 }else{ err.stock <- c(err.stock,"\n For example, the ") }
105 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
106 " do not appear in the variable metadata file:\n")
107 identif <- id3[which(!(id3%in%id4))][1:min(3,length(which(!(id3%in%id4))))]
108 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
109 }
110 if(length(which(id4%in%id3))!=length(id4)){
111 if(length(which(!(id4%in%id3)))<4){ err.stock <- c(err.stock,"\n The ")
112 }else{ err.stock <- c(err.stock,"\n For example, the ") }
113 err.stock <- c(err.stock,"following identifiers found in the variable metadata file\n",
114 " do not appear in the data matrix:\n")
115 identif <- id4[which(!(id4%in%id3))][1:min(3,length(which(!(id4%in%id3))))]
116 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
117 }
118 }
119
120 if(length(err.stock)!=0){ err.stock <- c(err.stock,"\nPlease check your data.\n") }
121
122 return(err.stock)
123
124 }