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comparison transformation_script.R @ 0:eacea1349a7c draft

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
author ethevenot
date Fri, 29 Jul 2016 12:11:01 -0400
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children d9e05021553c
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-1:000000000000 0:eacea1349a7c
1 ## Etienne Thevenot
2 ## W4M Core Development Team
3 ## etienne.thevenot@cea.fr
4 ## 2015-04-25
5
6 transformF <- function(datMN,
7 metC) {
8
9 ## options
10
11 optStrAsFacL <- options()[["stringsAsFactors"]]
12 options(stringsAsFactors = FALSE)
13
14 ## transformation
15
16 switch(metC,
17 log2 = {
18
19 cat("\n'log2' transformation\n", sep="")
20
21 if(length(which(datMN < 0)))
22 stop("The 'dataMatrix' contains negative values")
23
24 zerMN <- datMN == 0
25
26 ## Number of missing values
27 nasN <- length(which(is.na(datMN)))
28 cat("\nMissing values in the 'dataMatrix': ",
29 nasN,
30 " (",
31 round(nasN / cumprod(dim(datMN))[2] * 100),
32 "%)\n",
33 sep="")
34
35 ## Number of zero values
36 zerN <- length(which(zerMN))
37 cat("\nZero values in the 'dataMatrix': ",
38 zerN,
39 " (",
40 round(zerN / cumprod(dim(datMN))[2] * 100),
41 "%)\n",
42 sep="")
43
44 trfMN <- log2(1 + datMN)
45
46 },
47 log10 = {
48
49 cat("\n'log10' transformation\n", sep="")
50
51 if(length(which(datMN < 0)))
52 stop("The 'dataMatrix' contains negative values")
53
54 zerMN <- datMN == 0
55
56 ## Number of missing values
57 nasN <- length(which(is.na(datMN)))
58 cat("\nMissing values in the 'dataMatrix': ",
59 nasN,
60 " (",
61 round(nasN / cumprod(dim(datMN))[2] * 100),
62 "%)\n",
63 sep="")
64
65 ## Number of zero values
66 zerN <- length(which(zerMN))
67 cat("\nZero values in the 'dataMatrix': ",
68 zerN,
69 " (",
70 round(zerN / cumprod(dim(datMN))[2] * 100),
71 "%)\n",
72 sep="")
73
74 trfMN <- log10(1 + datMN)
75
76 }) ## end of 'log10' method
77
78
79 ## returning
80
81 options(stringsAsFactors=optStrAsFacL)
82
83 return(trfMN)
84
85 } ## end of transformF