Mercurial > repos > davidvanzessen > mutation_analysis

comparison sequence_overview.r @ 87:fd63f5307962 draft

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Uploaded
author davidvanzessen
date Mon, 30 May 2016 06:49:13 -0400
parents 0011a0597685
children d57c624a9aa9
comparison
equal deleted inserted replaced
86:0011a0597685 87:fd63f5307962
21 21
22 dat = merge(sequences, genes, by="Sequence.ID") 22 dat = merge(sequences, genes, by="Sequence.ID")
23 23
24 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] 24 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
25 25
26 dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT) 26 #dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT)
27 dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT)
27 28
28 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")] 29 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
29 IDs$best_match = as.character(IDs$best_match) 30 IDs$best_match = as.character(IDs$best_match)
30 31
31 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")]) 32 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
32 33
33 dat = data.frame(table(dat$seq_conc, dat$Functionality)) 34 dat = data.frame(table(dat$seq_conc, dat$Functionality))
34 35
35 dat = dat[dat$Freq > 1,] 36 #dat = dat[dat$Freq > 1,]
36 37
37 names(dat) = c("seq_conc", "Functionality", "Freq") 38 names(dat) = c("seq_conc", "Functionality", "Freq")
38 39
39 dat$seq_conc = factor(dat$seq_conc) 40 dat$seq_conc = factor(dat$seq_conc)
40 41
63 64
64 classes = c(nrow(ca1), nrow(ca2), nrow(cg1), nrow(cg2), nrow(cg3), nrow(cg4), nrow(cm)) 65 classes = c(nrow(ca1), nrow(ca2), nrow(cg1), nrow(cg2), nrow(cg3), nrow(cg4), nrow(cm))
65 66
66 classes.sum = sum(classes) 67 classes.sum = sum(classes)
67 68
68 if(!any(classes != 0 & classes != classes.sum)){ 69 if(classes.sum == 1){
69 next 70 next
70 } 71 }
71 72
72 id = as.numeric(dat[i,"seq_conc"]) 73 id = as.numeric(dat[i,"seq_conc"])
73 74