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adeschen merged 3 commits into from
Oct 7, 2025
Merged

Version bump in devel #617

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b753f2d
RAIDS 1.7.2: Replace GenomeInfoDb with Seqinfo in Suggests
hpages Jul 31, 2025
fce9d5a
Merge remote-tracking branch 'origin/main'
Oct 7, 2025
3a182eb
Version bump in devel
Oct 7, 2025
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -9,7 +9,7 @@ Description: This package implements specialized algorithms that enable
following publication: Belleau, P et al. Genetic Ancestry Inference from
Cancer-Derived Molecular Data across Genomic and Transcriptomic
Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
Version: 1.7.1
Version: 1.7.3
Authors@R: c(person("Pascal", "Belleau", email="pascal_belleau@hotmail.com",
role=c("cre", "aut"), comment = c(ORCID = "0000-0002-0802-1071")),
person("Astrid", "Deschênes", email="adeschen@hotmail.com",
Expand Down Expand Up @@ -51,7 +51,7 @@ Suggests: testthat,
rmarkdown,
BiocStyle,
withr,
GenomeInfoDb,
Seqinfo,
BSgenome.Hsapiens.UCSC.hg38,
EnsDb.Hsapiens.v86
BugReports: https://github.com/KrasnitzLab/RAIDS/issues
Expand Down
4 changes: 2 additions & 2 deletions R/RAIDS.R
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Expand Up @@ -694,12 +694,12 @@ NULL
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#' runExomeAncestry(pedStudy=demoPedigreeEx1, studyDF=studyDF,
Expand Down
10 changes: 5 additions & 5 deletions R/allelicFraction.R
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Expand Up @@ -69,16 +69,16 @@
#'
#' The `chrInfo` parameter contains the length of the chromosomes. The
#' length of the chromosomes can be obtain through the
#' \code{\link[GenomeInfoDb]{seqlengths}}
#' \code{\link[Seqinfo]{seqlengths}}
#' library.
#'
#' As example, for hg38 genome:
#'
#' ```
#'
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' }
#'
#' ```
Expand Down Expand Up @@ -107,12 +107,12 @@
#' profileGDS <- openfn.gds(fileProfile, readonly=FALSE)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## Estimate the allelic fraction of the pruned SNVs
#' estimateAllelicFraction(gdsReference=gds1KG, gdsProfile=profileGDS,
Expand Down
16 changes: 8 additions & 8 deletions R/allelicFraction_internal.R
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Expand Up @@ -314,13 +314,13 @@ getTableSNV <- function(gdsReference, gdsSample, currentProfile, studyID,
#' gds1KG <- snpgdsOpen(fileGDS)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <-
#' GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## Data frame with SNV information for the specified chromosome (chr 1)
#' snpInfo <- data.frame(cnt.tot=c(41, 17, 27, 15, 11, 37, 16, 32),
Expand Down Expand Up @@ -725,12 +725,12 @@ computeAlleleFraction <- function(snpPos, w=10, cutOff=-3) {
#' profileGDS <- openfn.gds(fileProfile)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## The function returns a data frame containing the allelic fraction info
#' result <- RAIDS:::computeAllelicFractionDNA(gdsReference=gds1KG,
Expand Down Expand Up @@ -938,12 +938,12 @@ computeAllelicFractionDNA <- function(gdsReference, gdsSample, currentProfile,
#' profileGDS <- openfn.gds(fileProfile)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## The function returns a data frame containing the allelic fraction info
#' result <- RAIDS:::computeAllelicFractionRNA(gdsReference=gds1KG,
Expand Down Expand Up @@ -1101,12 +1101,12 @@ computeAllelicFractionRNA <- function(gdsReference, gdsSample, gdsRefAnnot,
#' gds1KG <- snpgdsOpen(fileGDS)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## Data frame with SNV information for the specified chromosome (chr 1)
#' snpInfo <- data.frame(cnt.tot=c(41, 17, 27, 15, 11, 37, 16, 32),
Expand Down
20 changes: 10 additions & 10 deletions R/processStudy.R
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Expand Up @@ -2013,12 +2013,12 @@ computeAncestryFromSyntheticFile <- function(gdsReference, gdsProfile,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#'
Expand Down Expand Up @@ -2301,12 +2301,12 @@ runExomeAncestry <- function(pedStudy, studyDF, pathProfileGDS,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#'
Expand Down Expand Up @@ -2616,12 +2616,12 @@ inferAncestry <- function(profileFile, pathProfileGDS,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#'
Expand Down Expand Up @@ -2823,12 +2823,12 @@ inferAncestryDNA <- function(profileFile, pathProfileGDS,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#'
Expand Down Expand Up @@ -3136,12 +3136,12 @@ runRNAAncestry <- function(pedStudy, studyDF, pathProfileGDS,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \donttest{
#'
Expand Down
24 changes: 12 additions & 12 deletions R/processStudy_internal.R
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Expand Up @@ -386,12 +386,12 @@ validateComputePoolSyntheticAncestryGr <- function(gdsProfile, sampleRM,
#' "GDS_Sample_with_study_demo.gds"), readonly=TRUE)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## The validation should be successful
#' RAIDS:::validateEstimateAllelicFraction(gdsReference=gds1KG,
Expand Down Expand Up @@ -1152,12 +1152,12 @@ validateAdd1KG2SampleGDS <- function(gdsReference, gdsProfileFile,
#' Diagnosis=c("Cancer", "Cancer"), Source=c("TCGA", "TCGA"))
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' ## Profiles used for synthetic data set
#' syntheticRefDF <- data.frame(sample.id=c("HG00150", "HG00138", "HG00330",
Expand Down Expand Up @@ -2219,12 +2219,12 @@ selParaPCAUpQuartile <- function(matKNN, pedCall, refCall,
#' closefn.gds(gdsReference)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' studyDFSyn <- data.frame(study.id=paste0(studyDF$study.id, ".Synthetic"),
#' study.desc=paste0(studyDF$study.id, " synthetic data"),
Expand Down Expand Up @@ -2623,12 +2623,12 @@ runProfileAncestry <- function(gdsReference, gdsRefAnnot, studyDF,
#' dataRef <- select1KGPopForSynthetic(fileReferenceGDS, nbProfiles=2L)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' studyDFSyn <- data.frame(study.id=paste0(studyDF$study.id, ".Synthetic"),
#' study.desc=paste0(studyDF$study.id, " synthetic data"),
Expand Down Expand Up @@ -3301,12 +3301,12 @@ computeAncestryFromSynthetic <- function(gdsReference, gdsProfile,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \dontrun{
#'
Expand Down Expand Up @@ -3875,12 +3875,12 @@ createProfile <- function(profileFile, profileName,
#' closefn.gds(gds1KG)
#'
#' ## Required library for this example to run correctly
#' if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
#' if (requireNamespace("Seqinfo", quietly=TRUE) &&
#' requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {
#'
#' ## Chromosome length information
#' ## chr23 is chrX, chr24 is chrY and chrM is 25
#' chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#' chrInfo <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]
#'
#' \dontrun{
#'
Expand Down
7 changes: 7 additions & 0 deletions inst/NEWS.md
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@@ -1,3 +1,10 @@
CHANGES IN VERSION 1.7.3
------------------------

BUG FIXES

o Change default parameters for snpgdsIBDKING() function

CHANGES IN VERSION 1.5.1
------------------------

Expand Down
4 changes: 2 additions & 2 deletions man/computeAllelicFractionDNA.Rd
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4 changes: 2 additions & 2 deletions man/computeAllelicFractionRNA.Rd
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4 changes: 2 additions & 2 deletions man/computeAllelicImbDNAChr.Rd
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4 changes: 2 additions & 2 deletions man/computeLOHBlocksDNAChr.Rd
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4 changes: 2 additions & 2 deletions man/demoPedigreeEx1.Rd
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