Mercurial > repos > melpetera > tablemerge
comparison TableMerge/tablemerge_script.R @ 0:902ab790fb7b draft
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author | melpetera |
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date | Thu, 23 Feb 2017 04:37:49 -0500 |
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-1:000000000000 | 0:902ab790fb7b |
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1 ################################################################################################ | |
2 # TABLE MERGE # | |
3 # # | |
4 # User: Galaxy # | |
5 # Starting date: 16-04-2015 # | |
6 # V-0.1: First version of merge code # | |
7 # V-0.2: Addition of data check and handling of special characters # | |
8 # # | |
9 # # | |
10 # Input files: dataMatrix ; Metadata file # | |
11 # Output files: dataMatrix ; Metadata file # | |
12 # # | |
13 # Dependencies: RcheckLibrary.R ; miniTools.R # | |
14 # # | |
15 ################################################################################################ | |
16 | |
17 # Parameters (for dev) | |
18 if(FALSE){ | |
19 DM.name <- "dataMatrix_CleanIons_CleanEch.txt" | |
20 meta.name <- "sampleMetadata_CleanEch.txt" | |
21 metype <- "sample" | |
22 output <- "Combined_${Metadata_in.name}" | |
23 } | |
24 | |
25 | |
26 | |
27 tab.merge <- function(DM.name,meta.name,metype,output){ | |
28 # This function allows to merge the dataMatrix with one metadata table. | |
29 # | |
30 # Parameters: | |
31 # - DM.name, meta.name: dataMatrix and metadata files' access respectively | |
32 # - metype: "sample" or "variable" depending on metadata content | |
33 # - output: output file's access | |
34 | |
35 | |
36 # Input -------------------------------------------------------------- | |
37 | |
38 DM <- read.table(DM.name,header=TRUE,sep="\t",check.names=FALSE) | |
39 meta <- read.table(meta.name,header=TRUE,sep="\t",check.names=FALSE,colClasses="character") | |
40 | |
41 # Table match check | |
42 table.check <- match2(DM,meta,metype) | |
43 check.err(table.check) | |
44 | |
45 # StockID | |
46 meta.id <- stockID(DM,meta,metype) | |
47 DM<-meta.id$dataMatrix ; meta<-meta.id$Metadata ; meta.id<-meta.id$id.match | |
48 | |
49 | |
50 # Merging tables ----------------------------------------------------- | |
51 | |
52 if(metype=="sample"){ | |
53 ori.DM <- DM | |
54 rownames(DM) <- DM[,1] | |
55 DM <- DM[,-1] | |
56 DM <- t(DM) | |
57 DM <- data.frame(sample=row.names(DM),DM,check.names=FALSE) | |
58 rownames(DM) <- NULL | |
59 } | |
60 | |
61 comb.data <- merge(x=meta,y=DM,by.x=1,by.y=1) | |
62 | |
63 | |
64 # Output ------------------------------------------------------------- | |
65 | |
66 # Getting back original identifiers | |
67 if(metype=="sample"){ | |
68 id.ori <- reproduceID(ori.DM,comb.data,metype,meta.id) | |
69 }else{ | |
70 id.ori <- reproduceID(DM,comb.data,metype,meta.id) | |
71 } | |
72 comb.data <- id.ori$Metadata | |
73 | |
74 # Writing the table | |
75 write.table(comb.data,output,sep="\t",quote=FALSE,row.names=FALSE) | |
76 | |
77 | |
78 } # End of tab.merge | |
79 | |
80 | |
81 # Typical function call | |
82 # tab.merge(DM.name,meta.name,metype,output) |