Commit 2a5bd340 authored by Dylan Aïssi's avatar Dylan Aïssi

New upstream version 1.18.0

parent ae5c4984
......@@ -6,7 +6,7 @@ Description: Contains data and functions that
sequence naming conventions (e.g., "chr1" versus "1"),
including a function that attempts to place sequence names in
their natural, rather than lexicographic, order.
Version: 1.16.0
Version: 1.18.0
Encoding: UTF-8
Author: Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
......@@ -25,5 +25,10 @@ Collate: utils.R rankSeqlevels.R assembly-utils.R loadTaxonomyDb.R
GenomeDescription-class.R mapGenomeBuilds.R zzz.R
VignetteBuilder: knitr
Video: http://youtu.be/wdEjCYSXa7w
git_url: https://git.bioconductor.org/packages/GenomeInfoDb
git_branch: RELEASE_3_8
git_last_commit: 1f0c4a2
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: no
Packaged: 2018-04-30 23:56:00 UTC; biocbuild
Packaged: 2018-10-31 00:04:33 UTC; biocbuild
......@@ -40,7 +40,7 @@ export(
standardChromosomes, keepStandardChromosomes,
## Seqinfo-class.R:
Seqinfo,
Seqinfo, checkCompatibleSeqinfo,
## GenomeDescription-classR:
GenomeDescription
......
CHANGES IN VERSION 1.18.0
-------------------------
NEW FEATURES
o Add checkCompatibleSeqinfo().
SIGNIFICANT USER-VISIBLE CHANGES
o Update genomeMappingTbl.csv, the db used internally by genomeBuilds()
and family.
CHANGES IN VERSION 1.14.0
-------------------------
......
......@@ -649,3 +649,10 @@ setMethod("intersect", c("Seqinfo", "Seqinfo"), function(x, y) {
merge(x, y)[intersect(seqnames(x), seqnames(y))]
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### checkCompatibleSeqinfo()
###
checkCompatibleSeqinfo <- function(x, y) merge(seqinfo(x), seqinfo(y))
No preview for this file type
The purpose of the files in GenomeInfoDb/inst/extdata/dataFiles is to support
seqlevelsStyle(). seqlevelsStyle() detects a chromosome naming style e.g. UCSC,
NCBI etc.
Many organisms follow the same naming style, whether the style is NCBI, UCSC or
Ensembl. For example, the chromosome set for Dog (Canis_familiaris.txt) is a
superset of the one for sheep. seqlevelsStyle() does the right thing on any
vector of chromosome names that follow the same naming style as Dog so it's not
necessary to add a file for Ovis_aries.txt.
Including these base files or supersets eliminates the need to include one
file for each organism we want to support in GenomeInfoDb.
This diff is collapsed.
......@@ -37,6 +37,8 @@
\alias{merge,Seqinfo,Seqinfo-method}
\alias{intersect,Seqinfo,Seqinfo-method}
\alias{checkCompatibleSeqinfo}
\title{Seqinfo objects}
\description{
......@@ -197,6 +199,13 @@
overlap operations.
}
}
A convenience wrapper, \code{checkCompatibleSeqinfo()}, is provided
for checking whether 2 objects have compatible seqinfo components
or not. \code{checkCompatibleSeqinfo(x, y)} is equivalent to
\code{merge(seqinfo(x), seqinfo(y))} so will work on any objects
\code{x} and \code{y} that support \code{\link{seqinfo}()}.
}
\author{H. Pagès}
......@@ -305,6 +314,17 @@ if (interactive()) {
stopifnot(identical(x, merge(x, Seqinfo())))
stopifnot(identical(x, merge(Seqinfo(), x)))
stopifnot(identical(x, merge(x, x)))
## ---------------------------------------------------------------------
## D. checkCompatibleSeqinfo()
## ---------------------------------------------------------------------
library(GenomicRanges)
gr1 <- GRanges("chr3:15-25", seqinfo=x)
gr2 <- GRanges("chr3:105-115", seqinfo=y)
if (interactive()) {
checkCompatibleSeqinfo(gr1, gr2) # raises an error
}
}
\keyword{methods}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment