Mercurial > repos > davidvanzessen > mutation_analysis

comparison sequence_overview.r @ 103:e21cbe15381f draft

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Uploaded
author davidvanzessen
date Tue, 21 Jun 2016 05:30:16 -0400
parents e6bc976760d4
children 603a10976e9c
comparison
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102:e6bc976760d4 103:e21cbe15381f
168 print(paste("Matched with unmatched:", some.unmatched)) 168 print(paste("Matched with unmatched:", some.unmatched))
169 print(paste("Count that should match 'matched' sequences:", matched)) 169 print(paste("Count that should match 'matched' sequences:", matched))
170 170
171 #ACGT overview 171 #ACGT overview
172 172
173 NToverview = merged 173 NToverview = merged[!grepl("^unmatched", merged$best_match),]
174 174
175 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq, sep="_") 175 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq, sep="_")
176 176
177 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq)) 177 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))
178 NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq)) 178 NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq))