Mercurial > repos > ethevenot > transformation
annotate transformation_script.R @ 3:cc0e9eff0de2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
author | ethevenot |
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date | Wed, 28 Feb 2018 09:15:47 -0500 |
parents | d9e05021553c |
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rev | line source |
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eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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1 ## Etienne Thevenot |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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2 ## W4M Core Development Team |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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3 ## etienne.thevenot@cea.fr |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
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4 ## 2015-04-25 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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5 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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6 transformF <- function(datMN, |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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7 metC) { |
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d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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8 |
0
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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9 ## options |
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d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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10 |
0
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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11 optStrAsFacL <- options()[["stringsAsFactors"]] |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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12 options(stringsAsFactors = FALSE) |
1
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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13 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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14 ## checking |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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15 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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16 if(length(which(datMN < 0))) { |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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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
ethevenot
parents:
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18 sink() |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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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
ethevenot
parents:
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20 } |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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21 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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22 ## Number of missing values |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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23 nasN <- length(which(is.na(datMN))) |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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24 cat("\nMissing values in the 'dataMatrix': ", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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25 nasN, |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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26 " (", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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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
ethevenot
parents:
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28 "%)\n", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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29 sep="") |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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diff
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30 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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31 ## Number of zero values |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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32 zerN <- length(which(datMN == 0)) |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
0
diff
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33 cat("\nZero values in the 'dataMatrix': ", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
0
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34 zerN, |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
0
diff
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35 " (", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
0
diff
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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
ethevenot
parents:
0
diff
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37 "%)\n", |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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38 sep="") |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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39 |
0
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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40 ## transformation |
1
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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41 |
0
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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42 switch(metC, |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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43 log2 = { |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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44 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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45 cat("\n'log2' transformation\n", sep="") |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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46 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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47 trfMN <- log2(1 + datMN) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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48 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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49 }, |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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50 log10 = { |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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51 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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52 cat("\n'log10' transformation\n", sep="") |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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53 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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54 trfMN <- log10(1 + datMN) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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55 |
1
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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56 }, |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
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57 sqrt = { |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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58 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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59 cat("\n'Square root' transformation\n", sep="") |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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60 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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61 trfMN <- sqrt(datMN) |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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62 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
parents:
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63 |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
ethevenot
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64 }) ## end of method |
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eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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parents:
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65 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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parents:
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66 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
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67 ## returning |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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68 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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69 options(stringsAsFactors=optStrAsFacL) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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70 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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71 return(trfMN) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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72 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
ethevenot
parents:
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73 } ## end of transformF |