From b753f2d82f5ba9faa787b2d2575e9f5bf3709a16 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= Date: Thu, 31 Jul 2025 10:55:01 -0700 Subject: [PATCH 1/2] RAIDS 1.7.2: Replace GenomeInfoDb with Seqinfo in Suggests --- DESCRIPTION | 4 ++-- R/RAIDS.R | 4 ++-- R/allelicFraction.R | 10 +++++----- R/allelicFraction_internal.R | 16 ++++++++-------- R/processStudy.R | 20 ++++++++++---------- R/processStudy_internal.R | 24 ++++++++++++------------ man/computeAllelicFractionDNA.Rd | 4 ++-- man/computeAllelicFractionRNA.Rd | 4 ++-- man/computeAllelicImbDNAChr.Rd | 4 ++-- man/computeLOHBlocksDNAChr.Rd | 4 ++-- man/demoPedigreeEx1.Rd | 4 ++-- man/estimateAllelicFraction.Rd | 10 +++++----- man/inferAncestry.Rd | 4 ++-- man/inferAncestryDNA.Rd | 4 ++-- man/inferAncestryGeneAware.Rd | 4 ++-- man/profileAncestry.Rd | 4 ++-- man/runExomeAncestry.Rd | 4 ++-- man/runProfileAncestry.Rd | 4 ++-- man/runRNAAncestry.Rd | 4 ++-- man/runWrapperAncestry.Rd | 4 ++-- man/validateEstimateAllelicFraction.Rd | 4 ++-- man/validateRunExomeOrRNAAncestry.Rd | 4 ++-- man/wrapperAncestry.Rd | 4 ++-- vignettes/RAIDS.Rmd | 6 +++--- vignettes/Wrappers.Rmd | 12 ++++++------ 25 files changed, 85 insertions(+), 85 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 969b5a478..9b58bdc41 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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: 1.7.2 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", @@ -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 diff --git a/R/RAIDS.R b/R/RAIDS.R index 4a04dcf18..203923893 100644 --- a/R/RAIDS.R +++ b/R/RAIDS.R @@ -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, diff --git a/R/allelicFraction.R b/R/allelicFraction.R index a37e1647f..acbd4dc8c 100644 --- a/R/allelicFraction.R +++ b/R/allelicFraction.R @@ -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] #' } #' #' ``` @@ -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, diff --git a/R/allelicFraction_internal.R b/R/allelicFraction_internal.R index 2481cde94..d43fba1f2 100644 --- a/R/allelicFraction_internal.R +++ b/R/allelicFraction_internal.R @@ -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), @@ -728,12 +728,12 @@ 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, @@ -946,12 +946,12 @@ 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, @@ -1109,12 +1109,12 @@ 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), diff --git a/R/processStudy.R b/R/processStudy.R index 580ea09d8..b1e78666c 100644 --- a/R/processStudy.R +++ b/R/processStudy.R @@ -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{ #' @@ -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{ #' @@ -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{ #' @@ -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{ #' @@ -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{ #' diff --git a/R/processStudy_internal.R b/R/processStudy_internal.R index e9a2799b5..2cd478009 100644 --- a/R/processStudy_internal.R +++ b/R/processStudy_internal.R @@ -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, @@ -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", @@ -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"), @@ -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"), @@ -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{ #' @@ -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{ #' diff --git a/man/computeAllelicFractionDNA.Rd b/man/computeAllelicFractionDNA.Rd index f8428788b..796e97b39 100644 --- a/man/computeAllelicFractionDNA.Rd +++ b/man/computeAllelicFractionDNA.Rd @@ -116,12 +116,12 @@ gds1KG <- snpgdsOpen(fileGDS) 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, diff --git a/man/computeAllelicFractionRNA.Rd b/man/computeAllelicFractionRNA.Rd index 1b60d3ebb..ba4ea9206 100644 --- a/man/computeAllelicFractionRNA.Rd +++ b/man/computeAllelicFractionRNA.Rd @@ -129,12 +129,12 @@ gdsRefAnnot <- openfn.gds(fileAnnotGDS) 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, diff --git a/man/computeAllelicImbDNAChr.Rd b/man/computeAllelicImbDNAChr.Rd index 7872acdd9..5eb2c36bf 100644 --- a/man/computeAllelicImbDNAChr.Rd +++ b/man/computeAllelicImbDNAChr.Rd @@ -69,12 +69,12 @@ fileGDS <- file.path(dataDir, "ex1_good_small_1KG.gds") 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), diff --git a/man/computeLOHBlocksDNAChr.Rd b/man/computeLOHBlocksDNAChr.Rd index d1bf63705..b008fd931 100644 --- a/man/computeLOHBlocksDNAChr.Rd +++ b/man/computeLOHBlocksDNAChr.Rd @@ -98,13 +98,13 @@ fileGDS <- file.path(dataDir, "ex1_good_small_1KG.gds") 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), diff --git a/man/demoPedigreeEx1.Rd b/man/demoPedigreeEx1.Rd index 0dea25bb8..d757d2f3c 100644 --- a/man/demoPedigreeEx1.Rd +++ b/man/demoPedigreeEx1.Rd @@ -106,12 +106,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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, diff --git a/man/estimateAllelicFraction.Rd b/man/estimateAllelicFraction.Rd index 953737d63..55af9fb89 100644 --- a/man/estimateAllelicFraction.Rd +++ b/man/estimateAllelicFraction.Rd @@ -95,15 +95,15 @@ the type of study (DNA or RNA). \details{ The \code{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{html}{\out{
}}\preformatted{ -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] \} }\if{html}{\out{
}} @@ -132,12 +132,12 @@ gds1KG <- snpgdsOpen(fileGDS) 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, diff --git a/man/inferAncestry.Rd b/man/inferAncestry.Rd index a139c6f27..68191a5e9 100644 --- a/man/inferAncestry.Rd +++ b/man/inferAncestry.Rd @@ -247,12 +247,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/inferAncestryDNA.Rd b/man/inferAncestryDNA.Rd index e5aeb0ba5..8374a3a4a 100644 --- a/man/inferAncestryDNA.Rd +++ b/man/inferAncestryDNA.Rd @@ -247,12 +247,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/inferAncestryGeneAware.Rd b/man/inferAncestryGeneAware.Rd index 27c7f9c09..e4364bb48 100644 --- a/man/inferAncestryGeneAware.Rd +++ b/man/inferAncestryGeneAware.Rd @@ -269,12 +269,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/profileAncestry.Rd b/man/profileAncestry.Rd index 3f2bfef23..7be61f3a1 100644 --- a/man/profileAncestry.Rd +++ b/man/profileAncestry.Rd @@ -278,12 +278,12 @@ set.seed(3043) 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"), diff --git a/man/runExomeAncestry.Rd b/man/runExomeAncestry.Rd index b2e9a0141..ec9420671 100644 --- a/man/runExomeAncestry.Rd +++ b/man/runExomeAncestry.Rd @@ -173,12 +173,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/runProfileAncestry.Rd b/man/runProfileAncestry.Rd index f578560e9..daca7ea0a 100644 --- a/man/runProfileAncestry.Rd +++ b/man/runProfileAncestry.Rd @@ -170,12 +170,12 @@ dataRef <- select1KGPop(gdsReference, nbProfiles=2L) 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"), diff --git a/man/runRNAAncestry.Rd b/man/runRNAAncestry.Rd index 712409b70..97c6c2d2e 100644 --- a/man/runRNAAncestry.Rd +++ b/man/runRNAAncestry.Rd @@ -178,12 +178,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/runWrapperAncestry.Rd b/man/runWrapperAncestry.Rd index 7f27cc776..3e73deaeb 100644 --- a/man/runWrapperAncestry.Rd +++ b/man/runWrapperAncestry.Rd @@ -182,12 +182,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/man/validateEstimateAllelicFraction.Rd b/man/validateEstimateAllelicFraction.Rd index 3c5eb7a51..bfb321242 100644 --- a/man/validateEstimateAllelicFraction.Rd +++ b/man/validateEstimateAllelicFraction.Rd @@ -101,12 +101,12 @@ gdsSample <- openfn.gds(file.path(dataDir, "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, diff --git a/man/validateRunExomeOrRNAAncestry.Rd b/man/validateRunExomeOrRNAAncestry.Rd index 52029c1bc..4e28b843b 100644 --- a/man/validateRunExomeOrRNAAncestry.Rd +++ b/man/validateRunExomeOrRNAAncestry.Rd @@ -103,12 +103,12 @@ ped <- data.frame(Name.ID=c("Sample_01", "Sample_02"), 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", diff --git a/man/wrapperAncestry.Rd b/man/wrapperAncestry.Rd index cda691b48..2bb7c5a2c 100644 --- a/man/wrapperAncestry.Rd +++ b/man/wrapperAncestry.Rd @@ -295,12 +295,12 @@ dataRef <- select1KGPop(gds1KG, nbProfiles=2L) 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{ diff --git a/vignettes/RAIDS.Rmd b/vignettes/RAIDS.Rmd index 235aca641..883dffcfd 100644 --- a/vignettes/RAIDS.Rmd +++ b/vignettes/RAIDS.Rmd @@ -333,9 +333,9 @@ In this example, the profile is from DNA source and requires the use of the ```{r infere, echo=TRUE, eval=TRUE, collapse=TRUE, warning=FALSE, message=FALSE} ########################################################################### -## GenomeInfoDb and BSgenome are required libraries to run this example +## Seqinfo and BSgenome are required libraries to run this example ########################################################################### -if (requireNamespace("GenomeInfoDb", quietly=TRUE) && +if (requireNamespace("Seqinfo", quietly=TRUE) && requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) { ####################################################################### @@ -343,7 +343,7 @@ if (requireNamespace("GenomeInfoDb", quietly=TRUE) && ## chr23 is chrX, chr24 is chrY and chrM is 25 ####################################################################### genome <- BSgenome.Hsapiens.UCSC.hg38::Hsapiens - chrInfo <- GenomeInfoDb::seqlengths(genome)[1:25] + chrInfo <- Seqinfo::seqlengths(genome)[1:25] ####################################################################### ## The demo SNP VCF file of the DNA profile donor diff --git a/vignettes/Wrappers.Rmd b/vignettes/Wrappers.Rmd index 664b92656..a51703a73 100644 --- a/vignettes/Wrappers.Rmd +++ b/vignettes/Wrappers.Rmd @@ -261,13 +261,13 @@ gds1KG <- snpgdsOpen(fileGDS) dataRef <- select1KGPop(gds1KG, nbProfiles=2L) closefn.gds(gds1KG) -## GenomeInfoDb and BSgenome are required libraries to run this example -if (requireNamespace("GenomeInfoDb", quietly=TRUE) && +## Seqinfo and BSgenome are required libraries to run this example +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 path where the Sample GDS files (one per sample) @@ -525,13 +525,13 @@ gds1KG <- snpgdsOpen(fileGDS) dataRef <- select1KGPop(gds1KG, nbProfiles=2L) closefn.gds(gds1KG) -## GenomeInfoDb and BSgenome are required libraries to run this example -if (requireNamespace("GenomeInfoDb", quietly=TRUE) && +## Seqinfo and BSgenome are required libraries to run this example +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 path where the Sample GDS files (one per sample) From 3a182ebc4dabdf0cc70362e74bc1efe9d7754151 Mon Sep 17 00:00:00 2001 From: belleau Date: Tue, 7 Oct 2025 16:32:58 -0400 Subject: [PATCH 2/2] Version bump in devel --- DESCRIPTION | 2 +- inst/NEWS.md | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9b58bdc41..a337f9732 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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: 1.7.2 +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", diff --git a/inst/NEWS.md b/inst/NEWS.md index dfc113acf..a7904a686 100644 --- a/inst/NEWS.md +++ b/inst/NEWS.md @@ -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 ------------------------