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commit c1b9488569eaa4255ec05816fab5822e40cec6ab Author: Graham Inggs <[email protected]> Date: Fri Oct 13 17:46:15 2017 +0200 Imported Upstream version 1.28.6 --- DESCRIPTION | 4 ++-- R/GenomicRanges-comparison.R | 3 ++- inst/doc/ExtendingGenomicRanges.pdf | Bin 103241 -> 103036 bytes inst/doc/GRanges_and_GRangesList_slides.pdf | Bin 250940 -> 250940 bytes inst/doc/GenomicRangesHOWTOs.pdf | Bin 195193 -> 195126 bytes inst/doc/GenomicRangesIntroduction.pdf | Bin 159460 -> 159556 bytes inst/doc/Ten_things_slides.pdf | Bin 138327 -> 138327 bytes man/GenomicRanges-comparison.Rd | 2 +- man/makeGRangesFromDataFrame.Rd | 8 +++++--- 9 files changed, 10 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4b2db37..7a8e09c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,7 +11,7 @@ Description: The ability to efficiently represent and manipulate genomic summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure. -Version: 1.28.5 +Version: 1.28.6 Encoding: UTF-8 Author: P. Aboyoun, H. Pagès, and M. Lawrence Maintainer: Bioconductor Package Maintainer <[email protected]> @@ -49,4 +49,4 @@ Collate: utils.R phicoef.R transcript-utils.R constraint.R tileGenome.R tile-methods.R genomicvars.R zzz.R RoxygenNote: 5.0.1.9000 NeedsCompilation: yes -Packaged: 2017-09-06 22:51:36 UTC; biocbuild +Packaged: 2017-10-03 22:49:24 UTC; biocbuild diff --git a/R/GenomicRanges-comparison.R b/R/GenomicRanges-comparison.R index 95ad0f1..a039f13 100644 --- a/R/GenomicRanges-comparison.R +++ b/R/GenomicRanges-comparison.R @@ -250,7 +250,8 @@ order_GenomicRanges <- function(x, decreasing=FALSE, ignore.strand=FALSE) ### ignored. ### 'method' is also ignored at the moment. setMethod("order", "GenomicRanges", - function(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix")) + function(..., na.last=TRUE, decreasing=FALSE, + method=c("auto", "shell", "radix")) { ## Turn off this warning for now since it triggers spurious warnings ## when calling sort() on a GRangesList object. The root of the diff --git a/inst/doc/ExtendingGenomicRanges.pdf b/inst/doc/ExtendingGenomicRanges.pdf index 209de0a..a128de4 100644 Binary files a/inst/doc/ExtendingGenomicRanges.pdf and b/inst/doc/ExtendingGenomicRanges.pdf differ diff --git a/inst/doc/GRanges_and_GRangesList_slides.pdf b/inst/doc/GRanges_and_GRangesList_slides.pdf index 2cb8e5d..59dab1f 100644 Binary files a/inst/doc/GRanges_and_GRangesList_slides.pdf and b/inst/doc/GRanges_and_GRangesList_slides.pdf differ diff --git a/inst/doc/GenomicRangesHOWTOs.pdf b/inst/doc/GenomicRangesHOWTOs.pdf index 7fb18db..baf21be 100644 Binary files a/inst/doc/GenomicRangesHOWTOs.pdf and b/inst/doc/GenomicRangesHOWTOs.pdf differ diff --git a/inst/doc/GenomicRangesIntroduction.pdf b/inst/doc/GenomicRangesIntroduction.pdf index 7d1266b..4577996 100644 Binary files a/inst/doc/GenomicRangesIntroduction.pdf and b/inst/doc/GenomicRangesIntroduction.pdf differ diff --git a/inst/doc/Ten_things_slides.pdf b/inst/doc/Ten_things_slides.pdf index 3b478a9..42b99cc 100644 Binary files a/inst/doc/Ten_things_slides.pdf and b/inst/doc/Ten_things_slides.pdf differ diff --git a/man/GenomicRanges-comparison.Rd b/man/GenomicRanges-comparison.Rd index 34752f5..616dda6 100644 --- a/man/GenomicRanges-comparison.Rd +++ b/man/GenomicRanges-comparison.Rd @@ -44,7 +44,7 @@ \S4method{is.unsorted}{GenomicRanges}(x, na.rm=FALSE, strictly=FALSE, ignore.strand=FALSE) -\S4method{order}{GenomicRanges}(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix")) +\S4method{order}{GenomicRanges}(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix")) \S4method{sort}{GenomicRanges}(x, decreasing=FALSE, ignore.strand=FALSE, by) diff --git a/man/makeGRangesFromDataFrame.Rd b/man/makeGRangesFromDataFrame.Rd index 899144e..bf392c8 100644 --- a/man/makeGRangesFromDataFrame.Rd +++ b/man/makeGRangesFromDataFrame.Rd @@ -203,19 +203,21 @@ makeGRangesFromDataFrame(df) if (require(rtracklayer)) { session <- browserSession() genome(session) <- "sacCer2" - query <- ucscTableQuery(session, "Most Conserved") + query <- ucscTableQuery(session, "Assembly") df <- getTable(query) ## A common pitfall is to forget that the UCSC Table Browser uses the ## "0-based start" convention: - gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE) + gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE, + start.field="chromStart", end.field="chromEnd") head(gr0) min(start(gr0)) ## The start positions need to be converted into 1-based positions, ## to adhere to the convention used in Bioconductor: gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE, - starts.in.df.are.0based=TRUE) + starts.in.df.are.0based=TRUE, + start.field="chromStart", end.field="chromEnd") head(gr1) } } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-genomicranges.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
