[BioC] BED2RangedData
R
robinmjelle at gmail.com
Wed Mar 27 16:34:38 CET 2013
It hast has the three required columns:
chr, chrStart, chrEnd, right?
I also tried the following file which is
the output from bamtobed in bedtools:
chr1 68003859 68003910 DJDP4KN1:
153:D1NRJACXX:3:1101:1661:2231
55 +
chrX 85661697 85661748 DJDP4KN1:
153:D1NRJACXX:3:1101:2319:2241
255 -
chr9 3014548 3014599 DJDP4KN1:
153:D1NRJACXX:3:1101:2854:2242 255
and got:
Error in
BED2RangedData("/media/seagate/seq/H3K27
ChipSeq/Project_Mjelle-ChIP-2012-11-06/
Sample_Mjelle-Chip-TCF7-Chip-Control/Mapped.bed",
:
No valid data.BED passed in, which is a
data frame as BED format file with at
least 3 fields in the order of: chromosome,
start and end. Optional fields are
name, score and strand etc. Please refer to
http://genome.ucsc.edu/FAQ/FAQformat#format1
for details.
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