Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 6:d001d0c05dbe draft
Uploaded
author | davidvanzessen |
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date | Fri, 16 Dec 2016 07:30:32 -0500 |
parents | bcec7bb4e089 |
children | 8cbc1a8d27ae |
comparison
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5:bcec7bb4e089 | 6:d001d0c05dbe |
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398 | 398 |
399 VandDCount$l = log(VandDCount$Length) | 399 VandDCount$l = log(VandDCount$Length) |
400 maxVD = data.frame(data.table(VandDCount)[, list(max=max(l)), by=c("Sample")]) | 400 maxVD = data.frame(data.table(VandDCount)[, list(max=max(l)), by=c("Sample")]) |
401 VandDCount = merge(VandDCount, maxVD, by.x="Sample", by.y="Sample", all.x=T) | 401 VandDCount = merge(VandDCount, maxVD, by.x="Sample", by.y="Sample", all.x=T) |
402 VandDCount$relLength = VandDCount$l / VandDCount$max | 402 VandDCount$relLength = VandDCount$l / VandDCount$max |
403 check = is.nan(VandDCount$relLength) | |
404 if(any(check)){ | |
405 VandDCount[check,"relLength"] = 0 | |
406 } | |
403 | 407 |
404 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name) | 408 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name) |
405 | 409 |
406 completeVD = merge(VandDCount, cartegianProductVD, by.x=c("Top.V.Gene", "Top.D.Gene"), by.y=c("Top.V.Gene", "Top.D.Gene"), all=TRUE) | 410 completeVD = merge(VandDCount, cartegianProductVD, by.x=c("Top.V.Gene", "Top.D.Gene"), by.y=c("Top.V.Gene", "Top.D.Gene"), all=TRUE) |
407 | 411 |
443 | 447 |
444 VandJCount$l = log(VandJCount$Length) | 448 VandJCount$l = log(VandJCount$Length) |
445 maxVJ = data.frame(data.table(VandJCount)[, list(max=max(l)), by=c("Sample")]) | 449 maxVJ = data.frame(data.table(VandJCount)[, list(max=max(l)), by=c("Sample")]) |
446 VandJCount = merge(VandJCount, maxVJ, by.x="Sample", by.y="Sample", all.x=T) | 450 VandJCount = merge(VandJCount, maxVJ, by.x="Sample", by.y="Sample", all.x=T) |
447 VandJCount$relLength = VandJCount$l / VandJCount$max | 451 VandJCount$relLength = VandJCount$l / VandJCount$max |
452 | |
453 check = is.nan(VandJCount$relLength) | |
454 if(any(check)){ | |
455 VandJCount[check,"relLength"] = 0 | |
456 } | |
448 | 457 |
449 cartegianProductVJ = expand.grid(Top.V.Gene = Vchain$v.name, Top.J.Gene = Jchain$v.name) | 458 cartegianProductVJ = expand.grid(Top.V.Gene = Vchain$v.name, Top.J.Gene = Jchain$v.name) |
450 | 459 |
451 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) | 460 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) |
452 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) | 461 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) |
487 | 496 |
488 DandJCount$l = log(DandJCount$Length) | 497 DandJCount$l = log(DandJCount$Length) |
489 maxDJ = data.frame(data.table(DandJCount)[, list(max=max(l)), by=c("Sample")]) | 498 maxDJ = data.frame(data.table(DandJCount)[, list(max=max(l)), by=c("Sample")]) |
490 DandJCount = merge(DandJCount, maxDJ, by.x="Sample", by.y="Sample", all.x=T) | 499 DandJCount = merge(DandJCount, maxDJ, by.x="Sample", by.y="Sample", all.x=T) |
491 DandJCount$relLength = DandJCount$l / DandJCount$max | 500 DandJCount$relLength = DandJCount$l / DandJCount$max |
501 | |
502 check = is.nan(DandJCount$relLength) | |
503 if(any(check)){ | |
504 DandJCount[check,"relLength"] = 0 | |
505 } | |
492 | 506 |
493 cartegianProductDJ = expand.grid(Top.D.Gene = Dchain$v.name, Top.J.Gene = Jchain$v.name) | 507 cartegianProductDJ = expand.grid(Top.D.Gene = Dchain$v.name, Top.J.Gene = Jchain$v.name) |
494 | 508 |
495 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) | 509 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) |
496 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) | 510 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) |