Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 98:5ffbf40cdd4b draft

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Uploaded
author davidvanzessen
date Thu, 16 Jun 2016 05:05:47 -0400
parents e39176ccddc8
children ade5cf6fd2dc
comparison
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97:6e8dfbe164c6 98:5ffbf40cdd4b
293 293
294 for(i in 1:length(genes)){ 294 for(i in 1:length(genes)){
295 matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i]) 295 matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i])
296 } 296 }
297 297
298 matrx = calculate_result(i + 1, ".*", dat, matrx, func, fname, name="all") 298 matrx = calculate_result(i + 1, ".*", dat[!grepl("unmatched", dat$best_match),], matrx, func, fname, name="all")
299 299
300 result = data.frame(matrx) 300 result = data.frame(matrx)
301 if(fname == "sum"){ 301 if(fname == "sum"){
302 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR") 302 row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR")
303 } else { 303 } else {