On Fri, Apr 16, 2010 at 10:23 AM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> 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
> pterry@huskers.unl.edu
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

