From 1d8779509abfaf9ba247cc54823d15f68bc35f56 Mon Sep 17 00:00:00 2001 From: Thomas Kuilman Date: Thu, 15 Jun 2017 12:11:08 +0200 Subject: [PATCH] Changes to documentation --- README.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/README.md b/README.md index 4e1c5ef..4f40734 100644 --- a/README.md +++ b/README.md @@ -226,6 +226,31 @@ In general, we advise to update to the latest versions of CopywriteR and CopyhelpeR in case of errors. If the problems persist, please refer below for troubleshooting purposes. +#### Bug +We have found out about a bug that is affecting situations where the number of +comparisons between samples and controls exceeds the total number of unique +samples AND controls. For instance, in the case below, the number of comparisons +(3) exceeds the total number of unique samples and controls (./C003.bam and +./C016.bam; thus 2) + + > sample.control + samples controls + 1 ./C003.bam ./C003.bam + 2 ./C016.bam ./C016.bam + 3 ./C003.bam ./C016.bam + +Error messages look like this: +Error in `[<-.data.frame`(`*tmp*`, , "off.target", value = c(X, X, : + replacement has Y rows, data has Z + +We have fixed this issue in the newest version of Bioconductor that is yet to be +released, and will try to incorporate this in the release version too. +Since different Bioconductor versions require different version of CopywriteR, +I have provided two versions on the release page (under V2.6.1.2) that solve +this issue. An alternative to installing the new package is to prevent the above +situation, which is usually possible too. Please contact us if you have more +questions. + #### Mm10 We have come to realise that there was an bug in CopyhelpeR version 1.0.0 which leads to an error when creating mm10 helper files using the preCopywriteR