Mercurial > repos > davidvanzessen > mutation_analysis
changeset 88:d57c624a9aa9 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 30 May 2016 10:11:20 -0400 |
| parents | fd63f5307962 |
| children | 480fdd383fdb |
| files | sequence_overview.r |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/sequence_overview.r Mon May 30 06:49:13 2016 -0400 +++ b/sequence_overview.r Mon May 30 10:11:20 2016 -0400 @@ -23,8 +23,8 @@ dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] -#dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT) -dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT) +dat$seq_conc = paste(dat$CDR1.IMGT, dat$FR2.IMGT, dat$CDR2.IMGT, dat$FR3.IMGT, dat$CDR3.IMGT) +#dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT) IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")] IDs$best_match = as.character(IDs$best_match) @@ -48,7 +48,7 @@ tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); } cat("<table border='1'>", file=main.html, append=F) -cat("<caption>CDR1+CDR2+CDR3+FR2+FR3 sequences that show up more than once</caption>", file=main.html, append=T) +cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T) cat("<tr><th>Sequence</th><th>Functionality</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T) for(i in 1:nrow(dat)){ @@ -125,7 +125,7 @@ NToverview = genes[,c("Sequence.ID", "best_match")] -sequences$seq = paste(sequences$CDR1.IMGT, sequences$CDR2.IMGT, sequences$FR2.IMGT, sequences$FR3.IMGT, sep="_") +sequences$seq = paste(sequences$CDR1.IMGT, sequences$FR2.IMGT, sequences$CDR2.IMGT, sequences$FR3.IMGT, sep="_") NToverview = merge(NToverview, sequences[,c("Sequence.ID", "seq")], by="Sequence.ID")