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Updated NEWS.
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lima1 committed Dec 7, 2023
1 parent a41f054 commit ddf99ff
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1 change: 1 addition & 0 deletions NEWS
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions R/filterVcf.R
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Expand Up @@ -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.")
}

Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion R/readAllelicCountsFile.R
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Expand Up @@ -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(
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2 changes: 1 addition & 1 deletion R/runAbsoluteCN.R
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Expand Up @@ -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.
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4 changes: 2 additions & 2 deletions R/setPriorVcf.R
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Expand Up @@ -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])
}
}
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2 changes: 1 addition & 1 deletion inst/extdata/PureCN.R
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Expand Up @@ -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,
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6 changes: 3 additions & 3 deletions man/filterVcfMuTect2.Rd

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2 changes: 1 addition & 1 deletion man/runAbsoluteCN.Rd

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