Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 20:9185c3dfc679 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 27 Jan 2017 03:44:18 -0500 |
| parents | 5d11c9139a55 |
| children | d5d203d38c8a |
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| 19:3ef457aa5df6 | 20:9185c3dfc679 |
|---|---|
| 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 | 598 |
| 599 write.table(res, file=paste("raw_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) | 599 write.table(res, file=paste("raw_clonality_", sample_id, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=F) |
| 600 write.table(as.matrix(res[,2:ncol(res)]), file=paste("raw_clonality2_", sample_id, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=F) | |
| 601 | |
| 602 res = read.table(paste("raw_clonality_", sample_id, ".txt", sep=""), header=F, sep="\t", quote="", stringsAsFactors=F, fill=T, comment.char="") | |
| 600 | 603 |
| 601 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) | 604 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) |
| 602 | 605 |
| 603 #print(infer.result) | 606 #print(infer.result) |
| 604 | 607 |
| 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) | 608 write.table(data.table(infer.result[[12]]), file=paste("lymphclon_clonality_", sample_id, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=F) |
| 606 | 609 |
| 607 res$type = rowSums(res[,2:ncol(res)]) | 610 res$type = rowSums(res[,2:ncol(res)]) |
| 608 | 611 |
| 609 coincidence.table = data.frame(table(res$type)) | 612 coincidence.table = data.frame(table(res$type)) |
| 610 colnames(coincidence.table) = c("Coincidence Type", "Raw Coincidence Freq") | 613 colnames(coincidence.table) = c("Coincidence Type", "Raw Coincidence Freq") |
| 611 write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) | 614 write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) |
| 612 } | 615 } |
| 613 } else if(clonality_method == "old") { | 616 } else if(clonality_method == "old") { |
| 614 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")]) | 617 clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")]) |
| 615 | 618 |
| 616 #write files for every coincidence group of >1 | 619 #write files for every coincidence group of >1 |