From aa57e464ede08d910c4fc4b8769c69a51f5c1687 Mon Sep 17 00:00:00 2001 From: Jocelyn Penington Date: Thu, 24 Oct 2024 15:47:29 +1100 Subject: [PATCH] copynumQDNAseq: remove smoothBy in segmentation because crashed on iGP3 --- Rtools/malDrugR/copynumQDNAseq.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Rtools/malDrugR/copynumQDNAseq.R b/Rtools/malDrugR/copynumQDNAseq.R index 5798425..a7fb7ec 100644 --- a/Rtools/malDrugR/copynumQDNAseq.R +++ b/Rtools/malDrugR/copynumQDNAseq.R @@ -170,7 +170,7 @@ copyNums <- correctBins(countsCorrected) copyNumsNormed <- normalizeBins(copyNums) ## Segment copynumbers and call as 'gain' or 'loss copyNumsSegmented <- segmentBins(copyNumsNormed, - transformFun = "sqrt", smoothBy = 5 + transformFun = "sqrt" ) copyNumCalls <- callBins(copyNumsSegmented, method = "cutoff", @@ -212,7 +212,7 @@ cn_seg_trimmed <- # remove ranges where all calls are the same, i.e. all equal to parent rowwise() |> dplyr::filter( - !n_distinct(c_across(callcols)) == 1 + n_distinct(c_across(all_of(callcols))) > 1 ) ## Write table of segmented CN calls to csv file