On Fri, Apr 16, 2010 at 10:23 AM, [email protected] < [email protected]> wrote:
> Dear bioc-sig-sequencing, > > I would like to create a '.bed' file with all 4 columns (the 4th being peak > depth) from a RangedData object. I created a RangedData object of chipseq > peak results: > > > head(counts_s8) > RangedData with 6 rows and 1 value column across 1 space > space ranges | ARAB8 > <character> <IRanges> | <integer> > 1 chr1 [3690, 3920] | 3460 > 2 chr1 [3956, 3974] | 152 > 3 chr1 [3989, 4034] | 397 > ... > > Following the rtracklayer vignette, > > > export(counts_s8, "counts_s8_only.bed") > > produced a '.bed' file with three columns: > > chr1 3689 3920 > chr1 3955 3974 > chr1 3988 4034 > ... > > The vignette suggests one can use the 'format' parameter to explicitly > specify a format, but checking the rtracklayer manual I don't find details? > Can someone indicate how I can end up with all 4 columns from the > RangedData object in the '.bed' file? > > > The 'format' is for the file format, not the layout of the BED file. When you call export(), export.bed() is called. In the help for that function, it says that the column needs to be named "score" for it to be output as the BED score. But btw, if you just add a 'score' on there, it's not valid BED. It would be bedGraph. Maybe that's the format you want? (and the column still needs to be named 'score'). Michael > > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.6.0 > [2] RCurl_1.3-0 > [3] bitops_1.0-4.1 > [4] BSgenome.Athaliana.TAIR.04232008_1.3.16 > [5] chipseq_0.2.1 > [6] ShortRead_1.4.0 > [7] lattice_0.17-26 > [8] BSgenome_1.14.2 > [9] Biostrings_2.14.10 > [10] IRanges_1.4.10 > > > Thanks, > P. Terry > [email protected] > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
