From c90836b7d5cd8efc31d336de1491e014d167e517 Mon Sep 17 00:00:00 2001 From: chanf10_roche Date: Mon, 4 Dec 2023 13:25:57 -0800 Subject: [PATCH 1/4] Update --- R/runAbsoluteCN.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/runAbsoluteCN.R b/R/runAbsoluteCN.R index b575de1..15fffd8 100644 --- a/R/runAbsoluteCN.R +++ b/R/runAbsoluteCN.R @@ -1145,6 +1145,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, list( candidates = candidate.solutions, results = results, + exon.lrs = exon.lrs, input = list(tumor = tumor.coverage.file, normal = normal.coverage.file, log.ratio = GRanges(normal[, 1], on.target = normal$on.target, log.ratio = log.ratio), log.ratio.sdev = sd.seg, mapd = mapd, vcf = vcf, sampleid = sampleid, From e807dfc712e2bfed76e7e081d03486ff2c6086d6 Mon Sep 17 00:00:00 2001 From: chanf10_roche Date: Wed, 6 Dec 2023 11:17:17 -0800 Subject: [PATCH 2/4] Retain exon.lrs --- R/runAbsoluteCN.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/runAbsoluteCN.R b/R/runAbsoluteCN.R index 15fffd8..44639e8 100644 --- a/R/runAbsoluteCN.R +++ b/R/runAbsoluteCN.R @@ -1154,6 +1154,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, mapping.bias.rho = if (is.null(rho) || all(is.na(rho))) NULL else mean(rho, na.rm = TRUE), vcf.field.prefix = vcf.field.prefix, interval.file = interval.file, + exon.lrs = exon.lrs, args = list( filterVcf = args.filterVcf[vapply(args.filterVcf, object.size, double(1)) < 1000], filterIntervals = args.filterIntervals[vapply(args.filterIntervals, object.size, double(1)) < 1000]) From f6ab9120a06cbd36f4ac5a3bb69869f05a849c78 Mon Sep 17 00:00:00 2001 From: chanf10_roche Date: Wed, 6 Dec 2023 11:18:37 -0800 Subject: [PATCH 3/4] Remove extra exon.lrs --- R/runAbsoluteCN.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/runAbsoluteCN.R b/R/runAbsoluteCN.R index 44639e8..31adc00 100644 --- a/R/runAbsoluteCN.R +++ b/R/runAbsoluteCN.R @@ -1145,7 +1145,6 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, list( candidates = candidate.solutions, results = results, - exon.lrs = exon.lrs, input = list(tumor = tumor.coverage.file, normal = normal.coverage.file, log.ratio = GRanges(normal[, 1], on.target = normal$on.target, log.ratio = log.ratio), log.ratio.sdev = sd.seg, mapd = mapd, vcf = vcf, sampleid = sampleid, From 576f7260ecfcf264d813bd02104664bf4e911d5b Mon Sep 17 00:00:00 2001 From: chanf10_roche Date: Thu, 7 Dec 2023 08:41:41 -0800 Subject: [PATCH 4/4] Rename to interval.lrs --- R/runAbsoluteCN.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/runAbsoluteCN.R b/R/runAbsoluteCN.R index 31adc00..8d45f92 100644 --- a/R/runAbsoluteCN.R +++ b/R/runAbsoluteCN.R @@ -1153,7 +1153,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL, mapping.bias.rho = if (is.null(rho) || all(is.na(rho))) NULL else mean(rho, na.rm = TRUE), vcf.field.prefix = vcf.field.prefix, interval.file = interval.file, - exon.lrs = exon.lrs, + interval.lrs = exon.lrs, args = list( filterVcf = args.filterVcf[vapply(args.filterVcf, object.size, double(1)) < 1000], filterIntervals = args.filterIntervals[vapply(args.filterIntervals, object.size, double(1)) < 1000])