Mercurial > repos > ethevenot > checkformat
annotate checkformat_script.R @ 3:80a38d36f946 draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
author | ethevenot |
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date | Thu, 11 Jan 2018 10:24:56 -0500 |
parents | e194eec8e70c |
children | 9590fac86f63 |
rev | line source |
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1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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1 ## Etienne Thevenot |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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2 ## CEA, MetaboHUB Paris |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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3 ## etienne.thevenot@cea.fr |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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4 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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5 |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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6 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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7 ## Reads the dataMatrix, sampleMetadata, and variableMetadata .tsv files |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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8 ## and checks the formats |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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9 readAndCheckF <- function(datFilC="dataMatrix.tsv", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
diff
changeset
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10 samFilC="sampleMetadata.tsv", |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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changeset
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11 varFilC="variableMetadata.tsv", |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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12 makNamL) { |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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13 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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14 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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15 ## options |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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16 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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17 optStrAsFacL <- options()[["stringsAsFactors"]] |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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18 options(stringsAsFactors = FALSE) |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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19 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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20 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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21 ## checking that the tables have no duplicated row or column names |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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22 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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23 for(tabC in c("dat", "sam", "var")) { |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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24 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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25 tabNamC <- switch(tabC, dat="dataMatrix", sam="sampleMetadata", var="variableMetadata") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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26 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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27 rowVc <- read.table(eval(parse(text=paste0(tabC, "FilC"))), |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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28 check.names = FALSE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
diff
changeset
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29 header = TRUE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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30 sep = "\t")[, 1] |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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31 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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32 colVc <- unlist(read.table(eval(parse(text=paste0(tabC, "FilC"))), |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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33 check.names = FALSE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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34 nrow=1, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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35 sep = "\t"))[-1] |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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36 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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37 if(any(duplicated(rowVc))) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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38 stop("The following row name(s) is/are duplicated in the ", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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39 tabNamC, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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40 " table: '", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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41 paste(rowVc[duplicated(rowVc)], collapse="', '"), "'", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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42 call.=FALSE) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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43 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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44 if(any(duplicated(colVc))) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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changeset
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45 stop("The following column name(s) is/are duplicated in the ", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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46 tabNamC, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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47 " table: '", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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48 paste(colVc[duplicated(colVc)], collapse="', '"), "'", |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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49 call.=FALSE) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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50 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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51 } |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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52 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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53 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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54 ## reading tables |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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55 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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56 datMN <- t(as.matrix(read.table(datFilC, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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57 check.names = FALSE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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58 header = TRUE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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59 row.names = 1, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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60 sep = "\t"))) |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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61 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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parents:
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62 samDF <- read.table(samFilC, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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63 check.names = FALSE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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64 header = TRUE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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65 row.names = 1, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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66 sep = "\t") |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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67 |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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68 varDF <- read.table(varFilC, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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69 check.names = FALSE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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70 header = TRUE, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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71 row.names = 1, |
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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72 sep = "\t") |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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73 |
1
e194eec8e70c
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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74 |
3
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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75 ## checking that dataMatrix is numeric and that the sample and variable numbers are coherent |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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76 |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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77 if(mode(datMN) != "numeric") { |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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78 stop("The dataMatrix is not of the 'numeric' type", |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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79 call. = FALSE) |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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80 } |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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81 |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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82 if(nrow(datMN) != nrow(samDF)) { |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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83 if(nrow(datMN) > nrow(samDF)) { |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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84 print(setdiff(rownames(datMN), rownames(samDF))) |
80a38d36f946
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents:
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85 stop("The sample names above from dataMatrix were not found in sampleMetadata") |
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86 } else { |
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87 print(setdiff(rownames(samDF), rownames(datMN))) |
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88 stop("The sample names above from sampleMetadata were not found in dataMatrix") |
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89 } |
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90 } |
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91 |
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92 if(ncol(datMN) != nrow(varDF)) { |
80a38d36f946
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93 if(ncol(datMN) > nrow(varDF)) { |
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94 print(setdiff(colnames(datMN), rownames(varDF))) |
80a38d36f946
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95 stop("The variable names above from dataMatrix were not found in variableMetadata") |
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96 } else { |
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97 print(setdiff(rownames(varDF), colnames(datMN))) |
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98 stop("The variable names above from variableMetadata were not found in dataMatrix") |
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99 } |
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100 } |
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101 |
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102 |
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103 ## making sample and variable names (optional) |
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104 |
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105 newL <- FALSE |
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106 |
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107 if(makNamL) { |
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108 |
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109 cat("\n\nMessage: Converting sample and variable names to the standard R format\n") |
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110 |
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111 rownames(datMN) <- make.names(rownames(datMN), unique = TRUE) |
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112 colnames(datMN) <- make.names(colnames(datMN), unique = TRUE) |
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113 rownames(samDF) <- make.names(rownames(samDF), unique = TRUE) |
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114 rownames(varDF) <- make.names(rownames(varDF), unique = TRUE) |
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115 |
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116 newL <- TRUE |
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117 |
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118 } |
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119 |
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120 |
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121 ## checking sample and variable names |
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122 |
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123 chkL <- TRUE |
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124 |
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125 if(!identical(rownames(datMN), rownames(samDF))) { |
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126 |
3
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127 if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) { |
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128 |
3
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129 cat("\n\nMessage: Re-ordering dataMatrix sample names to match sampleMetadata\n") |
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130 datMN <- datMN[rownames(samDF), , drop = FALSE] |
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131 |
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132 stopifnot(identical(sort(rownames(datMN)), sort(rownames(samDF)))) |
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133 |
3
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134 newL <- TRUE |
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135 |
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136 } else { |
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137 |
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138 cat("\n\nStop: The sample names of dataMatrix and sampleMetadata do not match:\n") |
1
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139 print(cbind.data.frame(indice = 1:nrow(datMN), |
3
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140 dataMatrix=rownames(datMN), |
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141 sampleMetadata=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) |
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142 chkL <- FALSE |
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143 |
1
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144 } |
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145 |
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146 } |
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147 |
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148 if(!identical(colnames(datMN), rownames(varDF))) { |
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149 |
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150 if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) { |
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151 |
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152 cat("\n\nMessage: Re-ordering dataMatrix variable names to match variableMetadata\n") |
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153 datMN <- datMN[, rownames(varDF), drop = FALSE] |
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154 |
3
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155 stopifnot(identical(sort(colnames(datMN)), sort(rownames(varDF)))) |
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156 |
3
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157 newL <- TRUE |
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158 |
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159 } else { |
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160 |
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161 cat("\n\nStop: The variable names of dataMatrix and variableMetadata do not match:\n") |
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162 print(cbind.data.frame(indice = 1:ncol(datMN), |
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163 dataMatrix=colnames(datMN), |
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164 variableMetadata=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE]) |
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165 chkL <- FALSE |
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166 |
1
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167 } |
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168 |
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169 } |
3
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170 |
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171 |
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172 options(stringsAsFactors=optStrAsFacL) |
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173 |
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174 resLs <- list(chkL=chkL, |
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175 newL = newL, |
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176 datMN = datMN, |
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177 samDF = samDF, |
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178 varDF = varDF) |
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179 |
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180 return(resLs) |
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181 |
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182 } ## end of checkAndReadF |
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183 |
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184 |
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185 |
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186 |
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187 ## if(!identical(rownames(datMN), rownames(samDF))) { |
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188 ## ## checking sample names |
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189 |
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190 ## chkL <- FALSE |
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191 |
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192 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF)) |
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193 |
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194 ## if(length(datSamDifVc)) { |
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195 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="") |
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196 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))), |
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197 ## name = datSamDifVc)) |
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198 ## } |
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199 |
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200 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN)) |
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201 |
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202 ## if(length(samDatDifVc)) { |
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203 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="") |
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204 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))), |
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205 ## name = samDatDifVc)) |
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206 ## } |
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207 |
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208 ## if(nrow(datMN) != nrow(samDF)) { |
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209 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="") |
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210 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) { |
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211 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="") |
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212 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) { |
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213 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="") |
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214 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) { |
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215 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="") |
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216 ## print(cbind.data.frame(indice = 1:nrow(datMN), |
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217 ## dataMatrix_columnnames=rownames(datMN), |
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218 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) |
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219 ## } else { |
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220 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="") |
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221 ## print(cbind.data.frame(indice = 1:nrow(datMN), |
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222 ## dataMatrix_columnnames=rownames(datMN), |
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223 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) |
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224 ## } |
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225 |
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226 ## } |
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227 ## datRowVc <- rownames(datMN) |
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228 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) |
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229 ## if(datRowMakVc != datRowVc) { |
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230 ## rownames(datMN) <- datRowMakVc |
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231 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n") |
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232 ## } |
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233 |
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234 ## datColVc <- colnames(datMN) |
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235 ## datColMakVc <- make.names(datColVc, unique = TRUE) |
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236 ## if(datColMakVc != datColVc) { |
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237 ## colnames(datMN) <- datColMakVc |
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238 ## cat("\n\nMessage: The variable names of the dataMatrix have been converted to the standard R format\n") |
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239 ## } |
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240 |
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241 ## samRowVc <- rownames(datMN) |
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242 ## samRowMakVc <- make.names(samRowVc, unique = TRUE) |
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243 ## if(samRowMakVc != samRowVc) { |
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244 ## rownames(datMN) <- samRowMakVc |
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245 ## cat("\n\nMessage: The sample names of the sampleMetadata have been converted to the standard R format\n") |
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246 ## } |
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247 |
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248 ## datRowVc <- rownames(datMN) |
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249 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) |
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250 ## if(datRowMakVc != datRowVc) { |
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251 ## rownames(datMN) <- datRowMakVc |
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252 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n") |
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253 ## } |
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254 |
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255 ## } |
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256 |
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257 ## checking names (optional) |
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258 |
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259 |
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260 |
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261 |
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262 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) |
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263 ## if(datRowMakVc != datRowVc) { |
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264 ## if(makNamL) { |
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265 ## rownames(datMN) <- datRowMakVc |
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266 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format; select the make names argument to convert them\n") |
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267 ## } else { |
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268 ## cat("\n\nWarning: Some of the sample names of the dataMatrix are not in the standard R format; select the make names argument to convert them\n") |
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269 ## } |
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270 |
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271 ## if(makNamL) { |
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272 |
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273 ## rownames(datMN) <- make.names(rownames(datMN), unique = TRUE) |
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274 ## colnames(datMN) <- make.names(colnames(datMN), unique = TRUE) |
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275 ## rownames(samDF) <- make.names(rownames(samDF), unique = TRUE) |
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276 ## rownames(varDF) <- make.names(rownames(varDF), unique = TRUE) |
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277 |
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278 ## } |
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279 ## checking sample names |
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280 |
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281 ## if(nrow(datMN) == nrow(samDF)) { |
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282 |
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283 |
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284 |
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285 ## } |
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286 |
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287 ## chkL <- FALSE |
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288 |
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289 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF)) |
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290 |
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291 ## if(length(datSamDifVc)) { |
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292 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="") |
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293 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))), |
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294 ## name = datSamDifVc)) |
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295 ## } |
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296 |
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297 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN)) |
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298 |
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299 ## if(length(samDatDifVc)) { |
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300 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="") |
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301 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))), |
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302 ## name = samDatDifVc)) |
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303 ## } |
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304 |
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305 ## if(nrow(datMN) != nrow(samDF)) { |
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306 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="") |
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307 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) { |
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308 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="") |
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309 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) { |
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310 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="") |
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311 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) { |
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312 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="") |
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313 ## print(cbind.data.frame(indice = 1:nrow(datMN), |
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314 ## dataMatrix_columnnames=rownames(datMN), |
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315 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) |
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316 ## } else { |
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317 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="") |
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318 ## print(cbind.data.frame(indice = 1:nrow(datMN), |
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319 ## dataMatrix_columnnames=rownames(datMN), |
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320 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) |
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321 ## } |
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322 |
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323 ## } |
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324 |
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325 |
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326 ## if(!identical(colnames(datMN), rownames(varDF))) { |
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327 ## ## checking variable names |
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328 |
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329 ## chkL <- FALSE |
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330 |
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331 ## datVarDifVc <- setdiff(colnames(datMN), rownames(varDF)) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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332 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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333 ## if(length(datVarDifVc)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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334 ## cat("\nThe following variables were found in the dataMatrix row names but not in the variableMetadata row names:\n", sep="") |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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335 ## print(cbind.data.frame(row = as.numeric(sapply(datVarDifVc, function(varC) which(colnames(datMN) == varC))), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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336 ## name = datVarDifVc)) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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337 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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338 ## } |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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339 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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340 ## varDatDifVc <- setdiff(rownames(varDF), colnames(datMN)) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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341 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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342 ## if(length(varDatDifVc)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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343 ## cat("\n\nThe following variables were found in the variableMetadata row names but not in the dataMatrix row names:\n", sep="") |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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344 ## print(cbind.data.frame(row = as.numeric(sapply(varDatDifVc, function(varC) which(rownames(varDF) == varC))), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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345 ## name = varDatDifVc)) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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346 ## } |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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347 |
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348 ## if(ncol(datMN) != nrow(varDF)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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349 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " rows (ie variables) whereas the variableMetadata has ", nrow(varDF), " rows\n", sep="") |
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350 ## } else if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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351 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not in the same order:\n", sep="") |
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352 ## print(cbind.data.frame(row = 1:ncol(datMN), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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353 ## dataMatrix_rownames=colnames(datMN), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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354 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE]) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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355 ## } else { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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356 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not identical:\n", sep="") |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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357 ## print(cbind.data.frame(row = 1:ncol(datMN), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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358 ## dataMatrix_rownames=colnames(datMN), |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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359 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE]) |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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360 ## } |
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361 ## } |
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362 ## checkF <- function(datInpMN, |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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363 ## samInpDF, |
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364 ## varInpDF) { |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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365 |
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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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366 ## mode(datInpMN) == "numeric" && |
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367 ## identical(rownames(datInpMN), rownames(samInpDF)) && |
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368 ## identical(colnames(datInpMN), rownames(varInpDF)) |
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369 |
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370 |
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371 ## } |