[BioC] BED2RangedData

[Zhu, Lihua (Julie)]

Hi,

Here is code that should work for you.

YourPeaks = 
BED2RangedData(read.table("/media/seagate/seq/H3K27ChipSeq/Project_Mjelle-Ch
IP-2012-11-06/Sample_Mjelle-Chip-TCF7-Chip-Control/Mapped.bed",sep="\t",
header=FALSE))

Please let me know it works out for you. Thanks!

Best regards,

Julie


On 3/27/13 11:34 AM, "R" <robinmjelle at gmail.com> wrote:

> 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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