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commit 8feeb5efc8c42c2cab796a86b3449706e12efd4d Author: Andreas Tille <[email protected]> Date: Thu Nov 9 09:54:11 2017 +0100 New upstream version 1.46.0 --- DESCRIPTION | 8 ++++---- R/BSgenome-class.R | 4 +--- R/ODLT_SNPlocs-class.R | 18 ++++++++++-------- R/OldFashionSNPlocs-class.R | 12 ++++++------ R/OnDiskLongTable-class.R | 2 +- R/SNPlocs-class.R | 4 +--- R/XtraSNPlocs-class.R | 14 ++++++++------ build/vignette.rds | Bin 337 -> 337 bytes inst/doc/BSgenomeForge.pdf | Bin 252283 -> 252463 bytes inst/doc/GenomeSearching.pdf | Bin 191602 -> 191530 bytes man/SNPlocs-class.Rd | 34 ++++++++-------------------------- man/XtraSNPlocs-class.Rd | 36 +++++++++++++++--------------------- 12 files changed, 54 insertions(+), 78 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3166d87..3cf7941 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,15 +3,15 @@ Title: Software infrastructure for efficient representation of full genomes and their SNPs Description: Infrastructure shared by all the Biostrings-based genome data packages. -Version: 1.44.2 +Version: 1.46.0 Encoding: UTF-8 Author: Hervé Pagès Maintainer: H. Pagès <[email protected]> biocViews: Genetics, Infrastructure, DataRepresentation, SequenceMatching, Annotation, SNP Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= - 0.9.36), IRanges (>= 2.1.33), GenomeInfoDb (>= 1.11.4), - GenomicRanges (>= 1.27.6), Biostrings (>= 2.35.3), rtracklayer + 0.9.36), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.13.1), + GenomicRanges (>= 1.29.14), Biostrings (>= 2.35.3), rtracklayer (>= 1.25.8) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, @@ -35,4 +35,4 @@ Collate: utils.R OnDiskLongTable_old-class.R OnDiskLongTable-class.R BSgenomeViews-class.R BSgenome-utils.R export-methods.R BSgenomeForge.R NeedsCompilation: no -Packaged: 2017-09-22 22:31:36 UTC; biocbuild +Packaged: 2017-10-30 22:44:38 UTC; biocbuild diff --git a/R/BSgenome-class.R b/R/BSgenome-class.R index c7c17c7..1f5fe55 100644 --- a/R/BSgenome-class.R +++ b/R/BSgenome-class.R @@ -191,7 +191,7 @@ setMethod("seqinfo", "BSgenome", ### only supports replacement of the sequence names, i.e., except for their ### sequence names, Seqinfo objects 'value' and 'seqinfo(x)' must be identical. setReplaceMethod("seqinfo", "BSgenome", - function(x, new2old=NULL, force=FALSE, + function(x, new2old=NULL, pruning.mode=c("error", "coarse", "fine", "tidy"), value) { @@ -199,8 +199,6 @@ setReplaceMethod("seqinfo", "BSgenome", stop("the supplied 'seqinfo' must be a Seqinfo object") IN_THIS_CONTEXT <- paste0("when replacing the 'seqinfo' ", "of a BSgenome object") - if (!identical(force, FALSE)) - stop("'force' not supported ", IN_THIS_CONTEXT) pruning.mode <- match.arg(pruning.mode) if (pruning.mode != "error") stop("'pruning.mode' not supported ", IN_THIS_CONTEXT) diff --git a/R/ODLT_SNPlocs-class.R b/R/ODLT_SNPlocs-class.R index 84327af..a1ac083 100644 --- a/R/ODLT_SNPlocs-class.R +++ b/R/ODLT_SNPlocs-class.R @@ -121,15 +121,19 @@ setMethod("snplocs", "ODLT_SNPlocs", setMethod("snpsBySeqname", "ODLT_SNPlocs", .snpsBySeqname_ODLT_SNPlocs) -.snpsByOverlaps_ODLT_SNPlocs <- function(x, ranges, - maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), - drop.rs.prefix=FALSE, ...) +.snpsByOverlaps_ODLT_SNPlocs <- function(x, ranges, drop.rs.prefix=FALSE, ...) { ranges <- normarg_ranges(ranges) if (!isTRUEorFALSE(drop.rs.prefix)) stop(wmsg("'drop.rs.prefix' must be TRUE or FALSE")) - + dots <- list(...) + if (isTRUE(dots$invert)) + stop(wmsg("snpsByOverlaps() does not support 'invert=TRUE'")) + + if (is.null(maxgap <- dots$maxgap)) + maxgap <- -1L + if (is.null(minoverlap <- dots$minoverlap)) + minoverlap <- 0L df <- getBatchesByOverlapsFromOnDiskLongTable(x@snp_table, ranges, maxgap=maxgap, minoverlap=minoverlap, @@ -137,9 +141,7 @@ setMethod("snpsBySeqname", "ODLT_SNPlocs", .snpsBySeqname_ODLT_SNPlocs) x_spatial_index <- spatialIndex(x@snp_table) x_seqinfo <- seqinfo(x_spatial_index) gr0 <- .as_naked_GRanges(df, x_seqinfo) - idx <- which(overlapsAny(gr0, ranges, - maxgap=maxgap, minoverlap=minoverlap, - type=type, ...)) + idx <- which(overlapsAny(gr0, ranges, ...)) df <- df[idx, ] .as_GPos(df, x_seqinfo, drop.rs.prefix=drop.rs.prefix) } diff --git a/R/OldFashionSNPlocs-class.R b/R/OldFashionSNPlocs-class.R index c64f23b..6a137f1 100644 --- a/R/OldFashionSNPlocs-class.R +++ b/R/OldFashionSNPlocs-class.R @@ -447,11 +447,13 @@ setMethod("snpsBySeqname", "OldFashionSNPlocs", ) .snpsByOverlaps_OldFashionSNPlocs <- function(x, ranges, - maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), - drop.rs.prefix=FALSE, ...) + drop.rs.prefix=FALSE, ...) { ranges <- normarg_ranges(ranges) + dots <- list(...) + if (isTRUE(dots$invert)) + stop(wmsg("snpsByOverlaps() does not support 'invert=TRUE'")) + ## The only purpose of the line below is to check that 'x' and 'ranges' ## are based on the same reference genome (merge() will raise an error ## if they are not). @@ -461,9 +463,7 @@ setMethod("snpsBySeqname", "OldFashionSNPlocs", snps_by_seqname <- .snpsBySeqname_OldFashionSNPlocs(x, seqlevels(ranges), drop.rs.prefix=drop.rs.prefix) - subsetByOverlaps(snps_by_seqname, ranges, - maxgap=maxgap, minoverlap=minoverlap, - type=type, ...) + subsetByOverlaps(snps_by_seqname, ranges, ...) } setMethod("snpsByOverlaps", "OldFashionSNPlocs", diff --git a/R/OnDiskLongTable-class.R b/R/OnDiskLongTable-class.R index 05caf33..8eacaeb 100644 --- a/R/OnDiskLongTable-class.R +++ b/R/OnDiskLongTable-class.R @@ -712,7 +712,7 @@ getBatchesBySeqnameFromOnDiskLongTable <- function(x, seqnames, colidx=NULL, ### ranges: GenomicRanges object. ### colidx: integer or character vector of column indices, or NULL. getBatchesByOverlapsFromOnDiskLongTable <- function(x, ranges, - maxgap=0L, minoverlap=1L, + maxgap=-1L, minoverlap=0L, colidx=NULL, with.rowids=FALSE, as.data.frame=FALSE) diff --git a/R/SNPlocs-class.R b/R/SNPlocs-class.R index b4dc8d8..6981792 100644 --- a/R/SNPlocs-class.R +++ b/R/SNPlocs-class.R @@ -122,9 +122,7 @@ setGeneric("snpsBySeqname", signature="x", ### EXCEPT for 'minoverlap' default value that we set to zero so we also ### get SNPs that are insertions (relevant for XtraSNPlocs objects). setGeneric("snpsByOverlaps", signature="x", - function(x, ranges, maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), ...) - standardGeneric("snpsByOverlaps") + function(x, ranges, ...) standardGeneric("snpsByOverlaps") ) setGeneric("snpsById", signature="x", diff --git a/R/XtraSNPlocs-class.R b/R/XtraSNPlocs-class.R index 95b33f8..85feb39 100644 --- a/R/XtraSNPlocs-class.R +++ b/R/XtraSNPlocs-class.R @@ -335,12 +335,16 @@ setMethod("snpsBySeqname", "XtraSNPlocs", ### Arguments passed thru ... are further arguments to be passed to ### subsetByOverlaps(). setMethod("snpsByOverlaps", "XtraSNPlocs", - function(x, ranges, maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), + function(x, ranges, columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), - drop.rs.prefix=FALSE, as.DataFrame=FALSE, ...) + drop.rs.prefix=FALSE, as.DataFrame=FALSE, + ...) { ranges <- normarg_ranges(ranges) + dots <- list(...) + if (isTRUE(dots$invert)) + stop(wmsg("snpsByOverlaps() does not support 'invert=TRUE'")) + ## The only purpose of the line below is to check that 'x' and 'ranges' ## are based on the same reference genome (merge() will raise an error ## if they are not). @@ -352,9 +356,7 @@ setMethod("snpsByOverlaps", "XtraSNPlocs", snps_by_seqname <- snpsBySeqname(x, seqlevels(ranges), columns=columns, drop.rs.prefix=drop.rs.prefix) - ans <- subsetByOverlaps(snps_by_seqname, ranges, - maxgap=maxgap, minoverlap=minoverlap, - type=type, ...) + ans <- subsetByOverlaps(snps_by_seqname, ranges, ...) if (as.DataFrame) ans <- .to_DataFrame(ans, columns) ans diff --git a/build/vignette.rds b/build/vignette.rds index 1e3bf4e..7025cd5 100644 Binary files a/build/vignette.rds and b/build/vignette.rds differ diff --git a/inst/doc/BSgenomeForge.pdf b/inst/doc/BSgenomeForge.pdf index 9beecae..0562597 100644 Binary files a/inst/doc/BSgenomeForge.pdf and b/inst/doc/BSgenomeForge.pdf differ diff --git a/inst/doc/GenomeSearching.pdf b/inst/doc/GenomeSearching.pdf index 3e196b2..b041ae8 100644 Binary files a/inst/doc/GenomeSearching.pdf and b/inst/doc/GenomeSearching.pdf differ diff --git a/man/SNPlocs-class.Rd b/man/SNPlocs-class.Rd index ed849e1..2275cad 100644 --- a/man/SNPlocs-class.Rd +++ b/man/SNPlocs-class.Rd @@ -88,11 +88,8 @@ snpcount(x) snpsBySeqname(x, seqnames, ...) \S4method{snpsBySeqname}{SNPlocs}(x, seqnames, drop.rs.prefix=FALSE) -snpsByOverlaps(x, ranges, maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), ...) -\S4method{snpsByOverlaps}{SNPlocs}(x, ranges, maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), - drop.rs.prefix=FALSE, ...) +snpsByOverlaps(x, ranges, ...) +\S4method{snpsByOverlaps}{SNPlocs}(x, ranges, drop.rs.prefix=FALSE, ...) snpsById(x, ids, ...) \S4method{snpsById}{SNPlocs}(x, ids, ifnotfound=c("error", "warning", "drop")) @@ -110,8 +107,13 @@ snpsById(x, ids, ...) Additional arguments, for use in specific methods. Arguments passed to the \code{snpsByOverlaps} method for SNPlocs - objects thru \code{...} are passed to internal call to + objects thru \code{...} are used internally in the call to \code{\link[IRanges]{subsetByOverlaps}()}. + See \code{?IRanges::\link[IRanges]{subsetByOverlaps}} in the \pkg{IRanges} + package and \code{?GenomicRanges::\link[GenomicRanges]{subsetByOverlaps}} + in the \pkg{GenomicRanges} package for more information about the + \code{subsetByOverlaps()} generic and its method for + \link[GenomicRanges]{GenomicRanges} objects. } \item{drop.rs.prefix}{ Should the \code{rs} prefix be dropped from the returned RefSNP ids? @@ -124,16 +126,6 @@ snpsById(x, ids, ...) A single region of interest can be specified as a character string of the form \code{"ch14:5201-5300"}. } - \item{maxgap, minoverlap, type}{ - These arguments are passed to \code{\link[IRanges]{subsetByOverlaps}()} - which is used internally by \code{snpsByOverlaps}. - - Note that the default value for \code{minoverlap} is 0 which means - that, by default, in addition to the SNPs that are located \emph{within} - the genomic regions specified thru the \code{ranges} argument, - \code{snpsByOverlaps} also returns SNPs that are \emph{adjacent} to - these regions. Use \code{minoverlap=1L} to omit these SNPs. - } \item{ids}{ The RefSNP ids to look up (a.k.a. rs ids). Can be integer or character vector, with or without the \code{"rs"} prefix. NAs are not allowed. @@ -231,16 +223,6 @@ my_snps <- snpsByOverlaps(snps, my_cds) my_snps table(my_snps \%within\% my_cds) -## Note that, by default, in addition to the SNPs that are located -## within the regions of interest, snpsByOverlaps() also returns SNPs -## that are adjacent to these regions. Use 'minoverlap=1L' to omit these -## SNPs: -my_snps2 <- snpsByOverlaps(snps, my_cds, minoverlap=1) -table(my_snps2 \%within\% my_cds) - -## SNPs adjacent to the regions of interest: -setdiff(my_cds, my_snps2) - ## --------------------------------------------------------------------- ## snpsById() ## --------------------------------------------------------------------- diff --git a/man/XtraSNPlocs-class.Rd b/man/XtraSNPlocs-class.Rd index 72d0944..3a835af 100644 --- a/man/XtraSNPlocs-class.Rd +++ b/man/XtraSNPlocs-class.Rd @@ -55,19 +55,16 @@ \S4method{snpcount}{XtraSNPlocs}(x) \S4method{snpsBySeqname}{XtraSNPlocs}(x, seqnames, - columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), - drop.rs.prefix=FALSE, - as.DataFrame=FALSE) + columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), + drop.rs.prefix=FALSE, as.DataFrame=FALSE) -\S4method{snpsByOverlaps}{XtraSNPlocs}(x, ranges, maxgap=0L, minoverlap=0L, - type=c("any", "start", "end", "within", "equal"), - columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), - drop.rs.prefix=FALSE, as.DataFrame=FALSE, ...) +\S4method{snpsByOverlaps}{XtraSNPlocs}(x, ranges, + columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), + drop.rs.prefix=FALSE, as.DataFrame=FALSE, ...) \S4method{snpsById}{XtraSNPlocs}(x, ids, - columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), - ifnotfound=c("error", "warning", "drop"), - as.DataFrame=FALSE) + columns=c("seqnames", "start", "end", "strand", "RefSNP_id"), + ifnotfound=c("error", "warning", "drop"), as.DataFrame=FALSE) \S4method{colnames}{XtraSNPlocs}(x, do.NULL=TRUE, prefix="col") } @@ -101,12 +98,15 @@ object. A single region of interest can be specified as a character string of the form \code{"ch14:5201-5300"}. } - \item{maxgap, minoverlap, type}{ - These arguments are passed to \code{\link[IRanges]{subsetByOverlaps}()} - which is used internally by \code{snpsByOverlaps}. + \item{...}{ + Additional arguments, for use in specific methods. + + Arguments passed to the \code{snpsByOverlaps} method for XtraSNPlocs + objects thru \code{...} are used internally in the call to + \code{\link[IRanges]{subsetByOverlaps}()}. See \code{?IRanges::\link[IRanges]{subsetByOverlaps}} in the \pkg{IRanges} - package and \code{?GenomicRanges::\link[GenomicRanges]{subsetByOverlaps}} in - the \pkg{GenomicRanges} package for more information about the + package and \code{?GenomicRanges::\link[GenomicRanges]{subsetByOverlaps}} + in the \pkg{GenomicRanges} package for more information about the \code{subsetByOverlaps()} generic and its method for \link[GenomicRanges]{GenomicRanges} objects. } @@ -118,12 +118,6 @@ \item{ifnotfound}{ What to do if SNP ids are not found. } - \item{...}{ - Additional arguments, for use in specific methods. - Further arguments passed to the \code{snpsByOverlaps} method for - XtraSNPlocs objects (thru \code{...}) are passed to - \code{\link[IRanges]{subsetByOverlaps}()}. - } \item{do.NULL, prefix}{ These arguments are ignored. } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-bsgenome.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
