Mercurial > repos > davidvanzessen > shm_csr

comparison sequence_overview.r @ 31:fe44a905aee9 draft

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Uploaded
author davidvanzessen
date Tue, 13 Dec 2016 10:06:49 -0500
parents 3968d04b5724
children 4c5ba6b5d10d
comparison
equal deleted inserted replaced
30:33a7c49d48a7 31:fe44a905aee9
20 hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="") 20 hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="")
21 21
22 #before.unique = before.unique[!grepl("unmatched", before.unique$best_match),] 22 #before.unique = before.unique[!grepl("unmatched", before.unique$best_match),]
23 23
24 if(empty.region.filter == "leader"){ 24 if(empty.region.filter == "leader"){
25 before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) 25 before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
26 } else if(empty.region.filter == "FR1"){ 26 } else if(empty.region.filter == "FR1"){
27 before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) 27 before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
28 } else if(empty.region.filter == "CDR1"){ 28 } else if(empty.region.filter == "CDR1"){
29 before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) 29 before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
30 } else if(empty.region.filter == "FR2"){ 30 } else if(empty.region.filter == "FR2"){
31 before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) 31 before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
32 } 32 }
33 33
34 IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")] 34 IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
35 IDs$best_match = as.character(IDs$best_match) 35 IDs$best_match = as.character(IDs$best_match)
36 36