Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 8:fa240d1c57a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 18 Sep 2014 10:28:24 -0400
parents 68c6c7624ffc
children 58a28427930e
comparison
equal deleted inserted replaced
7:68c6c7624ffc 8:fa240d1c57a9
315 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 315 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
316 316
317 one = dat[dat$Patient == "VanDongen_cALL_14696.1",] 317 one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
318 two = dat[dat$Patient == "VanDongen_cALL_14696.2",] 318 two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
319 three = dat[dat$Patient == "VanDongen_cALL_14696.3",] 319 three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
320 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count") 320 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count", T)
321 321
322 one = dat[dat$Sample == "16278_Left",] 322 one = dat[dat$Sample == "16278_Left",]
323 two = dat[dat$Sample == "26402_Left",] 323 two = dat[dat$Sample == "26402_Left",]
324 three = dat[dat$Sample == "26759_Left",] 324 three = dat[dat$Sample == "26759_Left",]
325 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count") 325 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count", T)
326 326
327 one = dat[dat$Sample == "16278_Right",] 327 one = dat[dat$Sample == "16278_Right",]
328 two = dat[dat$Sample == "26402_Right",] 328 two = dat[dat$Sample == "26402_Right",]
329 three = dat[dat$Sample == "26759_Right",] 329 three = dat[dat$Sample == "26759_Right",]
330 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count") 330 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count", T)
331 331
332 332
333 interval = intervalFreq 333 interval = intervalFreq
334 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval)) 334 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
335 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 335 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
336 336
337 one = dat[dat$Patient == "VanDongen_cALL_14696.1",] 337 one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
338 two = dat[dat$Patient == "VanDongen_cALL_14696.2",] 338 two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
339 three = dat[dat$Patient == "VanDongen_cALL_14696.3",] 339 three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
340 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", T) 340 tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", F)
341 341
342 one = dat[dat$Sample == "16278_Left",] 342 one = dat[dat$Sample == "16278_Left",]
343 two = dat[dat$Sample == "26402_Left",] 343 two = dat[dat$Sample == "26402_Left",]
344 three = dat[dat$Sample == "26759_Left",] 344 three = dat[dat$Sample == "26759_Left",]
345 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", T) 345 tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", F)
346 346
347 one = dat[dat$Sample == "16278_Right",] 347 one = dat[dat$Sample == "16278_Right",]
348 two = dat[dat$Sample == "26402_Right",] 348 two = dat[dat$Sample == "26402_Right",]
349 three = dat[dat$Sample == "26759_Right",] 349 three = dat[dat$Sample == "26759_Right",]
350 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", T) 350 tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", F)
351 351
352 352
353 353