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annotate transformation_script.R @ 2:0ccfc3e15710 draft

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit b0373e2f4702a572450205419e2d64579c24c9ae
author ethevenot
date Tue, 06 Jun 2017 11:55:21 -0400
parents d9e05021553c
children
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eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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1 ## Etienne Thevenot
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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2 ## W4M Core Development Team
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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3 ## etienne.thevenot@cea.fr
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4 ## 2015-04-25
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eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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6 transformF <- function(datMN,
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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7 metC) {
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d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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9 ## options
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11 optStrAsFacL <- options()[["stringsAsFactors"]]
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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12 options(stringsAsFactors = FALSE)
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d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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14 ## checking
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16 if(length(which(datMN < 0))) {
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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17 cat("\nThe 'dataMatrix' contains negative values\n")
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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18 sink()
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19 stop("The 'dataMatrix' contains negative values", call. = FALSE)
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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20 }
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22 ## Number of missing values
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23 nasN <- length(which(is.na(datMN)))
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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24 cat("\nMissing values in the 'dataMatrix': ",
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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25 nasN,
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26 " (",
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27 round(nasN / cumprod(dim(datMN))[2] * 100),
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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28 "%)\n",
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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29 sep="")
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31 ## Number of zero values
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32 zerN <- length(which(datMN == 0))
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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33 cat("\nZero values in the 'dataMatrix': ",
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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34 zerN,
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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35 " (",
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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36 round(zerN / cumprod(dim(datMN))[2] * 100),
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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37 "%)\n",
d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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38 sep="")
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40 ## transformation
1
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0
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42 switch(metC,
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43 log2 = {
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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45 cat("\n'log2' transformation\n", sep="")
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47 trfMN <- log2(1 + datMN)
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49 },
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50 log10 = {
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52 cat("\n'log10' transformation\n", sep="")
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54 trfMN <- log10(1 + datMN)
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55
1
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56 },
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57 sqrt = {
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59 cat("\n'Square root' transformation\n", sep="")
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61 trfMN <- sqrt(datMN)
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64 }) ## end of method
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67 ## returning
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69 options(stringsAsFactors=optStrAsFacL)
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71 return(trfMN)
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73 } ## end of transformF