Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 41:a70dbcfa5d8a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 06 Jul 2017 09:07:52 -0400 |
| parents | 106275b54470 |
| children | 9a47d7a552d6 |
comparison
equal
deleted
inserted
replaced
| 40:106275b54470 | 41:a70dbcfa5d8a |
|---|---|
| 988 | 988 |
| 989 | 989 |
| 990 #generate the "Sequences that are present in more than one replicate" dataset | 990 #generate the "Sequences that are present in more than one replicate" dataset |
| 991 clonaltype.in.replicates = inputdata | 991 clonaltype.in.replicates = inputdata |
| 992 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),] | 992 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),] |
| 993 clonaltype.in.replicates = na.omit(clonaltype.in.replicates) | 993 clonaltype.in.replicates = clonaltype.in.replicates[!(is.na(clonaltype.in.replicates$ID) | is.na(clonaltype.in.replicates$Top.V.Gene) | is.na(clonaltype.in.replicates$Top.J.Gene)),] |
| 994 clonaltype = unlist(strsplit(clonaltype, ",")) | 994 clonaltype = unlist(strsplit(clonaltype, ",")) |
| 995 | 995 |
| 996 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":")) | 996 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":")) |
| 997 | 997 |
| 998 clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] | 998 clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] |
| 1000 clonaltype = clonaltype[-which(clonaltype == "Sample")] | 1000 clonaltype = clonaltype[-which(clonaltype == "Sample")] |
| 1001 | 1001 |
| 1002 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) | 1002 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) |
| 1003 clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] | 1003 clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] |
| 1004 | 1004 |
| 1005 | |
| 1006 write.table(clonaltype.in.replicates, "clonaltypes_replicates_before_table.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) | |
| 1007 | |
| 1005 clonaltype.counts = data.frame(table(clonaltype.in.replicates$clonaltype)) | 1008 clonaltype.counts = data.frame(table(clonaltype.in.replicates$clonaltype)) |
| 1009 | |
| 1010 write.table(clonaltype.counts, "clonaltypes_counts.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) | |
| 1011 | |
| 1006 names(clonaltype.counts) = c("clonaltype", "coincidence") | 1012 names(clonaltype.counts) = c("clonaltype", "coincidence") |
| 1007 | 1013 |
| 1008 clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] | 1014 clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] |
| 1009 | 1015 |
| 1010 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] | 1016 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] |