Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 17:da95be204ebc draft
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| author | davidvanzessen |
|---|---|
| date | Wed, 21 Dec 2016 05:57:31 -0500 |
| parents | 02efa5764a0a |
| children | 5d11c9139a55 |
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| 16:21ca9391a3b7 | 17:da95be204ebc |
|---|---|
| 592 clone_col_name = paste("V", replicate, sep="") | 592 clone_col_name = paste("V", replicate, sep="") |
| 593 colnames(clone_table) = c("paste", clone_col_name) | 593 colnames(clone_table) = c("paste", clone_col_name) |
| 594 res = merge(res, clone_table, by="paste", all=T) | 594 res = merge(res, clone_table, by="paste", all=T) |
| 595 } | 595 } |
| 596 | 596 |
| 597 res[is.na(res)] = 0 | 597 res[is.na(res)] = 0 |
| 598 | |
| 599 write.table(res, file=paste("raw_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) | |
| 600 | |
| 598 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) | 601 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) |
| 599 | 602 |
| 600 #print(infer.result) | 603 #print(infer.result) |
| 601 | 604 |
| 602 write.table(data.table(infer.result[[12]]), file=paste("lymphclon_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) | 605 write.table(data.table(infer.result[[12]]), file=paste("lymphclon_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) |
| 605 | 608 |
| 606 coincidence.table = data.frame(table(res$type)) | 609 coincidence.table = data.frame(table(res$type)) |
| 607 colnames(coincidence.table) = c("Coincidence Type", "Raw Coincidence Freq") | 610 colnames(coincidence.table) = c("Coincidence Type", "Raw Coincidence Freq") |
| 608 write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) | 611 write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) |
| 609 } | 612 } |
| 610 } else { | 613 } else if(clonality_method == "old") { |
| 611 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")]) | 614 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")]) |
| 612 | 615 |
| 613 #write files for every coincidence group of >1 | 616 #write files for every coincidence group of >1 |
| 614 samples = unique(clonalFreq$Sample) | 617 samples = unique(clonalFreq$Sample) |
| 615 for(sample in samples){ | 618 for(sample in samples){ |