VariantAnnotation 1.55.1: Depends on Seqinfo instead of GenomeInfoDb

Author: hpages

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Annotation of Genetic Variants
 Description: Annotate variants, compute amino acid coding changes,
         predict coding outcomes.
-Version: 1.55.0
+Version: 1.55.1
 Authors@R: c(
         person("Valerie", "Oberchain", role="aut"),
         person("Martin", "Morgan", role="aut"),
@@ -13,13 +13,13 @@ Authors@R: c(
                 email="maintainer@bioconductor.org"))
 License: Artistic-2.0
 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics,
-        GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5),
-        SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1)
+        Seqinfo, GenomicRanges (>= 1.61.1),
+        SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1)
 Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12),
-        IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2),
-        AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7),
-        BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3)
-Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
+        IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2),
+        AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1),
+        BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4)
+Suggests: GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
         TxDb.Hsapiens.UCSC.hg19.knownGene,
         SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132,
         SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,

NAMESPACE

@@ -7,7 +7,7 @@ import(BiocGenerics)
 importFrom(MatrixGenerics, rowRanges)
 import(S4Vectors)
 import(IRanges)
-import(GenomeInfoDb)
+import(Seqinfo)
 import(GenomicRanges)
 import(SummarizedExperiment)
 import(Rsamtools)

R/methods-VCF-class.R

@@ -472,7 +472,7 @@ SnpMatrixToVCF <- function(from, seqSource)
     ## match seqlevels style to seqSource
     map <- from$map
     chr <- as.character(map$chromosome)
-    seqlevelsStyle(chr) <- seqlevelsStyle(seqSource)
+    GenomeInfoDb::seqlevelsStyle(chr) <- GenomeInfoDb::seqlevelsStyle(seqSource)
     uniqueChr <- unique(chr)
     if (any(invalid <- !uniqueChr %in% seqlevels(seqSource)))
         stop("seqlevels not found in 'seqSource': ", 

inst/unitTests/test_VRanges-class.R

@@ -248,7 +248,7 @@ test_VRanges_vcf <- function() {
 
   vrA <- vr[sampleNames(vr) == "A"]
   runValue(sampleNames(vrA)) <- factor(runValue(sampleNames(vrA)))
-  vrA <- keepSeqlevels(vrA, unique(as.character(seqnames(vrA))))
+  seqlevels(vrA) <- unique(as.character(seqnames(vrA)))
   writeVcf(vrA, dest)
   vcfA <- readVcf(dest, genome = "hg19")
   vcfA.vr <- as(vcfA, "VRanges")

inst/unitTests/test_locateVariants-methods.R

@@ -31,7 +31,7 @@ test_locateVariants_queryAsVCF <- function()
 {
     fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
     vcf <- readVcf(fl, "hg19")
-    vcf <- renameSeqlevels(vcf, c("1" = "chr1"))
+    seqlevels(vcf) <- c("1" = "chr1")
     loc1 <- locateVariants(vcf, txdb, IntergenicVariants())
     loc2 <- locateVariants(rowRanges(vcf), txdb, IntergenicVariants())
     checkIdentical(loc1, loc2) 

man/VCF-class.Rd

@@ -464,13 +464,18 @@ identical(geno(vcf)$GQ, geno(vcf)[[2]])
 seqlevels(vcf)
 
 ## Rename the seqlevels to start with 'chr'.
-vcf2 <- renameSeqlevels(vcf, paste0("chr", seqlevels(vcf))) 
+vcf2 <- vcf
+seqlevels(vcf2) <- paste0("chr", seqlevels(vcf2))
 seqlevels(vcf2)
 
-## The VCF can also be subset by seqlevel using 'keepSeqlevels'
-## or 'dropSeqlevels'. See ?keepSeqlevels for details. 
-vcf3 <- keepSeqlevels(vcf2, "chr2", pruning.mode="coarse")
+## Dropping some of the seqlevels can have the effect of reducing
+## the length of the VCF object by keeping only its elements that
+## belong to the remaining seqlevels.
+vcf3 <- vcf2
+length(vcf3)
+seqlevels(vcf3, pruning.mode="coarse") <- "chr2"
 seqlevels(vcf3)
+length(vcf3)
 
 ## ----------------------------------------------------------------
 ## Header information 

man/filterVcf-methods.Rd

@@ -98,6 +98,8 @@ if (require(TxDb.Hsapiens.UCSC.hg19.knownGene)) {
   txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
   exons <- exons(txdb)
   exons22 <- exons[seqnames(exons) == "chr22"]
+
+  library(GenomeInfoDb)
   seqlevelsStyle(exons22) <- "NCBI"  ## match chrom names in VCF file
 
   ## Range-based filter:

man/locateVariants-methods.Rd

@@ -258,7 +258,7 @@ locateVariants(query, subject, region, ...)
   intersect(seqlevels(vcf), seqlevels(txdb))
 
   ## Rename seqlevels with renameSeqlevesl().
-  vcf <- renameSeqlevels(vcf, paste0("chr", seqlevels(vcf)))
+  seqlevels(vcf) <- paste0("chr", seqlevels(vcf))
 
   ## Confirm.
   intersect(seqlevels(vcf), seqlevels(txdb))

man/predictCoding-methods.Rd

@@ -191,7 +191,7 @@
   vcf <- readVcf(fl, "hg19")
 
   ## Rename seqlevels in the VCF object to match those in the TxDb.
-  vcf <- renameSeqlevels(vcf, "chr22")
+  seqlevels(vcf) <- "chr22"
   ## Confirm common seqlevels
   intersect(seqlevels(vcf), seqlevels(txdb))
 

man/seqinfo-method.Rd

@@ -28,7 +28,7 @@
 \author{Lori Shepherd}
 
 \seealso{
-  \code{\link{VcfFile}}, \code{\link[GenomeInfoDb]{Seqinfo}}
+  \code{\link{VcfFile}}, \code{\link[Seqinfo]{Seqinfo}}
 }
 
 \examples{