[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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