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1 ################################################################################################
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2 # TABLE MERGE #
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3 # #
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4 # User: Galaxy #
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5 # Starting date: 16-04-2015 #
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6 # V-0.1: First version of merge code #
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7 # V-0.2: Addition of data check and handling of special characters #
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8 # #
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9 # #
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10 # Input files: dataMatrix ; Metadata file #
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11 # Output files: dataMatrix ; Metadata file #
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12 # #
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13 # Dependencies: RcheckLibrary.R ; miniTools.R #
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14 # #
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15 ################################################################################################
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16
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17 # Parameters (for dev)
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18 if(FALSE){
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19 DM.name <- "dataMatrix_CleanIons_CleanEch.txt"
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20 meta.name <- "sampleMetadata_CleanEch.txt"
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21 metype <- "sample"
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22 output <- "Combined_${Metadata_in.name}"
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23 }
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24
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25
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26
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27 tab.merge <- function(DM.name,meta.name,metype,output){
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28 # This function allows to merge the dataMatrix with one metadata table.
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29 #
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30 # Parameters:
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31 # - DM.name, meta.name: dataMatrix and metadata files' access respectively
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32 # - metype: "sample" or "variable" depending on metadata content
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33 # - output: output file's access
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34
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35
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36 # Input --------------------------------------------------------------
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37
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38 DM <- read.table(DM.name,header=TRUE,sep="\t",check.names=FALSE)
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39 meta <- read.table(meta.name,header=TRUE,sep="\t",check.names=FALSE,colClasses="character")
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40
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41 # Table match check
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42 table.check <- match2(DM,meta,metype)
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43 check.err(table.check)
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44
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45 # StockID
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46 meta.id <- stockID(DM,meta,metype)
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47 DM<-meta.id$dataMatrix ; meta<-meta.id$Metadata ; meta.id<-meta.id$id.match
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48
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49
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50 # Merging tables -----------------------------------------------------
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51
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52 if(metype=="sample"){
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53 ori.DM <- DM
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54 rownames(DM) <- DM[,1]
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55 DM <- DM[,-1]
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56 DM <- t(DM)
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57 DM <- data.frame(sample=row.names(DM),DM,check.names=FALSE)
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58 rownames(DM) <- NULL
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59 }
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60
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61 comb.data <- merge(x=meta,y=DM,by.x=1,by.y=1)
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62
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63
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64 # Output -------------------------------------------------------------
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65
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66 # Getting back original identifiers
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67 if(metype=="sample"){
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68 id.ori <- reproduceID(ori.DM,comb.data,metype,meta.id)
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69 }else{
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70 id.ori <- reproduceID(DM,comb.data,metype,meta.id)
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71 }
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72 comb.data <- id.ori$Metadata
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73
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74 # Writing the table
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75 write.table(comb.data,output,sep="\t",quote=FALSE,row.names=FALSE)
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76
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77
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78 } # End of tab.merge
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79
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80
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81 # Typical function call
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82 # tab.merge(DM.name,meta.name,metype,output)
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