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?
> 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]
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