Dear all, I recently encountered an unexpected behavior of the GenomicRanges flank function. When using it with ignore.strand=TRUE the start argument seems to be ignored. > g <- GRanges("1", IRanges(1001, 2000), "+") > ranges(flank(g, 100, start=TRUE, ignore.strand=TRUE)) IRanges of length 1 start end width [1] 901 1000 100 > ranges(flank(g, 100, start=FALSE, ignore.strand=TRUE)) IRanges of length 1 start end width [1] 901 1000 100 I would have expected it to behave as in the case where there is no strand information: > h <- GRanges("1", IRanges(1001, 2000), "*") > ranges(flank(h, 100, start=TRUE)) IRanges of length 1 start end width [1] 901 1000 100 > ranges(flank(h, 100, start=FALSE)) IRanges of length 1 start end width [1] 2001 2100 100 Is this behavior intended? Any help or comments would be much appreciated. Leonard -- Leonard Goldstein, PhD Postdoctoral Research Fellow Department of Bioinformatics & Computational Biology Genentech, Inc. > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.13.7 IRanges_1.19.3 BiocGenerics_0.7.2 loaded via a namespace (and not attached): [1] stats4_3.0.0

Hi Leonard, Thanks for reporting the bug. The problem was that when 'ignore.strand=TRUE', 'start' was being set to TRUE. Now fixed in GenomicRanges 1.12.13 in release and 1.13.10 in devel. Both versions are available in svn now or through biocLite() Tuesday after 9am PST. Valerie On 05/09/2013 11:47 AM, Leonard Goldstein wrote: > Dear all, > > I recently encountered an unexpected behavior of the GenomicRanges flank function. > > When using it with ignore.strand=TRUE the start argument seems to be ignored. > >> g <- GRanges("1", IRanges(1001, 2000), "+") >> ranges(flank(g, 100, start=TRUE, ignore.strand=TRUE)) > IRanges of length 1 > start end width > [1] 901 1000 100 >> ranges(flank(g, 100, start=FALSE, ignore.strand=TRUE)) > IRanges of length 1 > start end width > [1] 901 1000 100 > > I would have expected it to behave as in the case where there is no strand information: > >> h <- GRanges("1", IRanges(1001, 2000), "*") >> ranges(flank(h, 100, start=TRUE)) > IRanges of length 1 > start end width > [1] 901 1000 100 >> ranges(flank(h, 100, start=FALSE)) > IRanges of length 1 > start end width > [1] 2001 2100 100 > > Is this behavior intended? Any help or comments would be much appreciated. > > Leonard > > -- > Leonard Goldstein, PhD > Postdoctoral Research Fellow > Department of Bioinformatics & Computational Biology > Genentech, Inc. > > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomicRanges_1.13.7 IRanges_1.19.3 BiocGenerics_0.7.2 > > loaded via a namespace (and not attached): > [1] stats4_3.0.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >