From ddf99ffbd510f242d7340bf983ac8b6a4552b43c Mon Sep 17 00:00:00 2001 From: Markus Riester Date: Thu, 7 Dec 2023 14:01:14 -0500 Subject: [PATCH] Updated NEWS. --- NEWS | 1 + R/filterVcf.R | 4 ++-- R/readAllelicCountsFile.R | 2 +- R/runAbsoluteCN.R | 2 +- R/setPriorVcf.R | 4 ++-- inst/extdata/PureCN.R | 2 +- man/filterVcfMuTect2.Rd | 6 +++--- man/runAbsoluteCN.Rd | 2 +- 8 files changed, 12 insertions(+), 11 deletions(-) diff --git a/NEWS b/NEWS index 3b613310..4038eb89 100755 --- a/NEWS +++ b/NEWS @@ -5,6 +5,7 @@ SIGNIFICANT USER-VISIBLE CHANGES o Provide interval-level likelihood scores in runAbsoluteCN return object. Thanks @tinyheero (#335). + o Documentation updates. Thanks @ddrichel (#325). BUGFIXES diff --git a/R/filterVcf.R b/R/filterVcf.R index ff4b0288..611bc3d1 100644 --- a/R/filterVcf.R +++ b/R/filterVcf.R @@ -223,7 +223,7 @@ interval.padding = 50, DB.info.flag = "DB") { } if (!is.null(info(vcf)[[DB.info.flag]]) && sum(info(vcf)[[DB.info.flag]]) < nrow(vcf) / 2) { - flog.warn("Less than half of variants are likely somatic. Make sure that VCF %s", + flog.warn("Less than half of variants are annoted as germline database member. Make sure that VCF %s", "contains both germline and somatic variants.") } @@ -523,7 +523,7 @@ function(vcf, tumor.id.in.vcf, allowed = 0.05) { newInfo <- DataFrame( Number = 0, Type = "Flag", - Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership", + Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or germline database membership", row.names = DB.info.flag) info(header(vcf)) <- rbind(info(header(vcf)), newInfo) info(vcf)[[DB.info.flag]] <- db diff --git a/R/readAllelicCountsFile.R b/R/readAllelicCountsFile.R index 357d9822..643bbd74 100644 --- a/R/readAllelicCountsFile.R +++ b/R/readAllelicCountsFile.R @@ -80,7 +80,7 @@ readAllelicCountsFile <- function(file, format, zero=NULL) { info(header(vcf)) <- DataFrame( Number = "0", Type = "Flag", - Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership", + Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or germline database membership", row.names = "DB") geno(header(vcf)) <- DataFrame( diff --git a/R/runAbsoluteCN.R b/R/runAbsoluteCN.R index 4f21b5a7..847dc6ec 100644 --- a/R/runAbsoluteCN.R +++ b/R/runAbsoluteCN.R @@ -29,7 +29,7 @@ #' @param vcf.file VCF file. #' Optional, but typically needed to select between local optima of similar #' likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf} -#' function. Requires a DB info flag for likely somatic status. The default +#' function. Requires a DB info flag for likely germline status. The default #' \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see #' \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again, #' do not expect very useful results without a VCF file. diff --git a/R/setPriorVcf.R b/R/setPriorVcf.R index 61866e54..f33211e1 100644 --- a/R/setPriorVcf.R +++ b/R/setPriorVcf.R @@ -60,14 +60,14 @@ setPriorVcf <- function(vcf, prior.somatic = c(0.5, 0.0005, 0.999, 0.0001, if (!is.null(info(vcf)[[Cosmic.CNT.info.field]])) { flog.info("Found COSMIC annotation in VCF. Requiring %i hits.", min.cosmic.cnt) - flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and likely somatic based on dbSNP membership or population allele frequency.", + flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and likely germline based on dbSNP membership or population allele frequency.", tmp[5], tmp[6]) prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt)] <- tmp[5] prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt & info(vcf)[[DB.info.flag]])] <- tmp[6] } else { - flog.info("Setting somatic prior probabilities for likely somatic hits to %f or to %f otherwise.", + flog.info("Setting somatic prior probabilities for likely germline hits to %f or to %f otherwise.", tmp[2], tmp[1]) } } diff --git a/inst/extdata/PureCN.R b/inst/extdata/PureCN.R index ab707e68..0ce5c3d9 100644 --- a/inst/extdata/PureCN.R +++ b/inst/extdata/PureCN.R @@ -105,7 +105,7 @@ option_list <- list( help = "Maximum considered ploidy [default %default]"), make_option(c("--max-copy-number"), action = "store", type = "double", default = max(eval(formals(PureCN::runAbsoluteCN)$test.num.copy)), - help = "Maximum allele-specific integer copy number, only used for fitting allele-specific copy numbers. Higher copy numbers might still be inferred and reported [default %default]"), + help = "Maximum allele-specific integer copy number, only used for fitting allele-specific copy numbers. Higher copy numbers are still be inferred and reported [default %default]"), make_option(c("--post-optimize"), action = "store_true", default = FALSE, help = "Post-optimization [default %default]"), make_option(c("--bootstrap-n"), action = "store", type = "integer", default = 0, diff --git a/man/filterVcfMuTect2.Rd b/man/filterVcfMuTect2.Rd index cdc54ea1..ab88998e 100644 --- a/man/filterVcfMuTect2.Rd +++ b/man/filterVcfMuTect2.Rd @@ -7,9 +7,9 @@ filterVcfMuTect2( vcf, tumor.id.in.vcf = NULL, - ignore = c("clustered_events", "t_lod", "str_contraction", "read_position", "position", - "fragment_length", "multiallelic", "clipping", "strand_artifact", "strand_bias", - "slippage", "weak_evidence", "orientation", "haplotype"), + ignore = c("clustered_events", "t_lod", "str_contraction", "read_position", + "position", "fragment_length", "multiallelic", "clipping", "strand_artifact", + "strand_bias", "slippage", "weak_evidence", "orientation", "haplotype"), ... ) } diff --git a/man/runAbsoluteCN.Rd b/man/runAbsoluteCN.Rd index 296e0d7b..7cb3aec5 100644 --- a/man/runAbsoluteCN.Rd +++ b/man/runAbsoluteCN.Rd @@ -98,7 +98,7 @@ deviation, used to model likelihood of sub-clonal copy number events.} \item{vcf.file}{VCF file. Optional, but typically needed to select between local optima of similar likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf} -function. Requires a DB info flag for likely somatic status. The default +function. Requires a DB info flag for likely germline status. The default \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again, do not expect very useful results without a VCF file.}