Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 37:f37e072affc0 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 19 Apr 2017 08:05:01 -0400 |
| parents | 7c33029fd63d |
| children | b6936fb52ab9 |
comparison
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| 36:edf2d5882b77 | 37:f37e072affc0 |
|---|---|
| 975 write.table(median.aa.l, "AAMedianBySample.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=F) | 975 write.table(median.aa.l, "AAMedianBySample.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=F) |
| 976 | 976 |
| 977 | 977 |
| 978 #generate the "Sequences that are present in more than one replicate" dataset | 978 #generate the "Sequences that are present in more than one replicate" dataset |
| 979 clonaltype.in.replicates = inputdata | 979 clonaltype.in.replicates = inputdata |
| 980 clonaltype.in.replicates = na.omit(clonaltype.in.replicates) | |
| 980 clonaltype = unlist(strsplit(clonaltype, ",")) | 981 clonaltype = unlist(strsplit(clonaltype, ",")) |
| 982 | |
| 983 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":")) | |
| 984 | |
| 985 clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] | |
| 986 | |
| 981 clonaltype = clonaltype[-which(clonaltype == "Sample")] | 987 clonaltype = clonaltype[-which(clonaltype == "Sample")] |
| 982 | 988 |
| 983 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) | 989 clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) |
| 984 clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] | 990 clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] |
| 985 | 991 |
| 988 | 994 |
| 989 clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] | 995 clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] |
| 990 | 996 |
| 991 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] | 997 clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] |
| 992 clonaltype.in.replicates = merge(clonaltype.in.replicates, clonaltype.counts, by="clonaltype") | 998 clonaltype.in.replicates = merge(clonaltype.in.replicates, clonaltype.counts, by="clonaltype") |
| 993 clonaltype.in.replicates = clonaltype.in.replicates[order(clonaltype.in.replicates$clonaltype),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] | 999 clonaltype.in.replicates = clonaltype.in.replicates[order(-clonaltype.in.replicates$coincidence, clonaltype.in.replicates$clonaltype, clonaltype.in.replicates$Replicate),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] |
| 1000 | |
| 994 | 1001 |
| 995 write.table(clonaltype.in.replicates, "clonaltypes_replicates.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) | 1002 write.table(clonaltype.in.replicates, "clonaltypes_replicates.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) |
| 996 | 1003 |
| 997 | 1004 |
| 998 | 1005 |