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annotate asca_w4m.R @ 0:93312041f1d5 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
author marie-tremblay-metatoul
date Fri, 21 Sep 2018 05:51:14 -0400
parents
children
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93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
1 asca_w4m <- function(datamatrix, samplemetadata, factors, variablemetadata, threshold, scaling="none", nPerm)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
2 {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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3 ## Transpose
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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4 # datamatrix <- t(datamatrix)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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5
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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6 # Check sample ID's
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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7 rownames(datamatrix) <- make.names(rownames(datamatrix), unique = TRUE)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
8 colnames(datamatrix) <- make.names(colnames(datamatrix), unique = TRUE)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
9 rownames(samplemetadata) <- make.names(rownames(samplemetadata), unique = TRUE)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
10 rownames(variablemetadata) <- make.names(rownames(variablemetadata), unique = TRUE)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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11
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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12 if(!identical(rownames(datamatrix), rownames(samplemetadata)))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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13 {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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14 if(identical(sort(rownames(datamatrix)), sort(rownames(samplemetadata))))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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15 {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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16 cat("\n\nMessage: Re-ordering dataMatrix sample names to match sampleMetadata\n")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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17 datamatrix <- datamatrix[rownames(samplemetadata), , drop = FALSE]
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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18 stopifnot(identical(sort(rownames(datamatrix)), sort(rownames(samplemetadata))))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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19 }else {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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20
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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21 cat("\n\nStop: The sample names of dataMatrix and sampleMetadata do not match:\n")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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22 print(cbind.data.frame(indice = 1:nrow(datamatrix),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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23 dataMatrix=rownames(datamatrix),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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24 sampleMetadata=rownames(samplemetadata))[rownames(datamatrix) != rownames(samplemetadata), , drop = FALSE])
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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25 }
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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26 }
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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28 # Check feature ID's
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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29 if(!identical(colnames(datamatrix), rownames(variablemetadata)))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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30 {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
31 if(identical(sort(colnames(datamatrix)), sort(rownames(variablemetadata))))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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32 {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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33 cat("\n\nMessage: Re-ordering dataMatrix variable names to match variableMetadata\n")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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34 datamatrix <- datamatrix[, rownames(variablemetadata), drop = FALSE]
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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35 stopifnot(identical(sort(colnames(datamatrix)), sort(rownames(variablemetadata))))
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
36 }else {
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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37 cat("\n\nStop: The variable names of dataMatrix and variableMetadata do not match:\n")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
38 print(cbind.data.frame(indice = 1:ncol(datamatrix),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff changeset
39 dataMatrix=colnames(datamatrix),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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40 variableMetadata=rownames(variablemetadata))[colnames(datamatrix) != rownames(variablemetadata), , drop = FALSE])
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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41 }
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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42 }
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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43
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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44 # Design
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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45 design <- data.matrix(samplemetadata[, colnames(samplemetadata) %in% factors])
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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46
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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47 # Scaling if scaling!=none
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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48 datamatrix <- prep(datamatrix, scaling)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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49
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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50 # Computation of the A-SCA model
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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51 data.asca <- ASCA.Calculate_w4m(datamatrix, design, scaling=scaling)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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52
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marie-tremblay-metatoul
parents:
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53 # Permutation test
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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54 data.asca.permutation <- ASCA.DoPermutationTest(data.asca[[1]], perm=nPerm)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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55 p <- c(data.asca.permutation, 0)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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56
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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57
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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58 # % of explained variance
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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59 ssq <- (data.asca[[2]]$summary.ssq)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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60 ssq <- cbind(round(rbind(ssq[2], ssq[3],ssq[4],ssq[5])*100, 2), p)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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61 rownames(ssq) <- c(factors[1], factors[2], "Interaction", "Residuals")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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62 colnames(ssq) <- c("% of explained variance", "Permutation p-value")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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63
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parents:
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64 # Add Scores and loadings at the end of meatadata files
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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65 noms <- colnames(samplemetadata)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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66 samplemetadata <- cbind(samplemetadata, (data.asca[[1]]$'1'$means.matrix + data.asca[[1]]$remainder) %*% data.asca[[1]]$'1'$svd$v[, 1:2],
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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67 (data.asca[[1]]$'2'$means.matrix + data.asca[[1]]$remainder) %*% data.asca[[1]]$'2'$svd$v[, 1:2],
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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68 (data.asca[[1]]$'12'$means.matrix + data.asca[[1]]$remainder) %*% data.asca[[1]]$'12'$svd$v[, 1:2])
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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69 colnames(samplemetadata) <- c(noms, paste(factors[1],"XSCOR-p1", sep="_"), paste(factors[1],"XSCOR-p2", sep="_"),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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70 paste(factors[2],"XSCOR-p1", sep="_"), paste(factors[2],"XSCOR-p2", sep="_"),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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71 "Interact_XSCOR-p1", "Interact_XSCOR-p2")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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72
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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73 noms <- colnames(variablemetadata)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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74 variablemetadata <- cbind(variablemetadata, data.asca[[1]]$'1'$svd$v[, 1:2], data.asca[[1]]$'2'$svd$v[, 1:2], data.asca[[1]]$'12'$svd$v[, 1:2])
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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75 colnames(variablemetadata) <- c(noms, paste(factors[1],"XLOAD-p1", sep="_"), paste(factors[1],"XLOAD-p2", sep="_"),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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76 paste(factors[2],"XLOAD-p1", sep="_"), paste(factors[2],"XLOAD-p2", sep="_"),
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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77 "Interact_XLOAD-p1", "Interact_XLOAD-p2")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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78
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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79 l <- list(data.asca[[1]], data.asca.permutation, ssq, samplemetadata, variablemetadata)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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80 names(l) <- c("ASCA","p-values", "ssq", "samplemetadata", "variablemetadata")
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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81 return(l)
93312041f1d5 planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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82 }