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annotate easyrlibrary-lib/RcheckLibrary.R @ 1:f64656ae9ea4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit b1f8bd1260c1c4b73600fb3867ca3bc613f258a7
author melpetera
date Sun, 09 Oct 2016 09:54:00 -0400
parents 71d83d8920bf
children
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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1 ######################################################
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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2 # R check library
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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3 # Coded by: M.Petera,
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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4 # - -
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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5 # R functions to use in R scripts
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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6 # (management of various generic subroutines)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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7 # - -
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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8 # V0: script structure + first functions
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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9 # V1: More detailed error messages in match functions
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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10 ######################################################
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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13 # Generic function to return an error if problems have been encountered - - - -
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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15 check.err <- function(err.stock){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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17 # err.stock = vector of results returned by check functions
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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19 if(length(err.stock)!=0){ stop("\n- - - - - - - - -\n",err.stock,"\n- - - - - - - - -\n") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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21 }
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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26 # Table match check functions - - - - - - - - - - - - - - - - - - - - - - - - -
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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28 # To check if dataMatrix and (variable or sample)Metadata match regarding identifiers
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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29 match2 <- function(dataMatrix, Metadata, Mtype){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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31 # dataMatrix = data.frame containing dataMatrix
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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32 # Metadata = data.frame containing sampleMetadata or variableMetadata
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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33 # Mtype = "sample" or "variable" depending on Metadata content
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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35 err.stock <- NULL # error vector
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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37 id2 <- Metadata[,1]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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38 if(Mtype=="sample"){ id1 <- colnames(dataMatrix)[-1] }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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39 if(Mtype=="variable"){ id1 <- dataMatrix[,1] }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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41 if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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42 err.stock <- c("\nData matrix and ",Mtype," metadata do not match regarding ",Mtype," identifiers.")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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43 if(length(which(id1%in%id2))!=length(id1)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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44 if(length(which(!(id1%in%id2)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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45 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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46 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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47 " do not appear in the ",Mtype," metadata file:\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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48 identif <- id1[which(!(id1%in%id2))][1:min(3,length(which(!(id1%in%id2))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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49 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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50 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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51 if(length(which(id2%in%id1))!=length(id2)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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52 if(length(which(!(id2%in%id1)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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53 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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54 err.stock <- c(err.stock,"following identifiers found in the ",Mtype," metadata file\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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55 " do not appear in the data matrix:\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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56 identif <- id2[which(!(id2%in%id1))][1:min(3,length(which(!(id2%in%id1))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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57 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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58 }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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59 err.stock <- c(err.stock,"\nPlease check your data.\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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60 }
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62 return(err.stock)
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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64 }
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66 # To check if the 3 standard tables match regarding identifiers
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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67 match3 <- function(dataMatrix, sampleMetadata, variableMetadata){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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69 # dataMatrix = data.frame containing dataMatrix
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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70 # sampleMetadata = data.frame containing sampleMetadata
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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71 # variableMetadata = data.frame containing variableMetadata
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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73 err.stock <- NULL # error vector
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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75 id1 <- colnames(dataMatrix)[-1]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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76 id2 <- sampleMetadata[,1]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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77 id3 <- dataMatrix[,1]
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78 id4 <- variableMetadata[,1]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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79
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80 if( length(which(id1%in%id2))!=length(id1) || length(which(id2%in%id1))!=length(id2) ){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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81 err.stock <- c(err.stock,"\nData matrix and sample metadata do not match regarding sample identifiers.")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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82 if(length(which(id1%in%id2))!=length(id1)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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83 if(length(which(!(id1%in%id2)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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84 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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85 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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86 " do not appear in the sample metadata file:\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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87 identif <- id1[which(!(id1%in%id2))][1:min(3,length(which(!(id1%in%id2))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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88 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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89 }
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90 if(length(which(id2%in%id1))!=length(id2)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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91 if(length(which(!(id2%in%id1)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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92 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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93 err.stock <- c(err.stock,"following identifiers found in the sample metadata file\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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94 " do not appear in the data matrix:\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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95 identif <- id2[which(!(id2%in%id1))][1:min(3,length(which(!(id2%in%id1))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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96 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
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97 }
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98 }
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99
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100 if( length(which(id3%in%id4))!=length(id3) || length(which(id4%in%id3))!=length(id4) ){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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101 err.stock <- c(err.stock,"\nData matrix and variable metadata do not match regarding variable identifiers.")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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102 if(length(which(id3%in%id4))!=length(id3)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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103 if(length(which(!(id3%in%id4)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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104 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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105 err.stock <- c(err.stock,"following identifiers found in the data matrix\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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106 " do not appear in the variable metadata file:\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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107 identif <- id3[which(!(id3%in%id4))][1:min(3,length(which(!(id3%in%id4))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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108 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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109 }
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110 if(length(which(id4%in%id3))!=length(id4)){
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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111 if(length(which(!(id4%in%id3)))<4){ err.stock <- c(err.stock,"\n The ")
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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112 }else{ err.stock <- c(err.stock,"\n For example, the ") }
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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113 err.stock <- c(err.stock,"following identifiers found in the variable metadata file\n",
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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114 " do not appear in the data matrix:\n")
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115 identif <- id4[which(!(id4%in%id3))][1:min(3,length(which(!(id4%in%id3))))]
71d83d8920bf planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit de79117e6ab856420b87efca3675c7963688f975
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116 err.stock <- c(err.stock," ",paste(identif,collapse="\n "),"\n")
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117 }
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118 }
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119
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120 if(length(err.stock)!=0){ err.stock <- c(err.stock,"\nPlease check your data.\n") }
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121
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122 return(err.stock)
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123
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124 }