[BioC] BED2RangedData

[Ou, Jianhong]

Yes, It must has the three required columns, and the 9 additional optional
columns must be the same order as the it defined. If you missed any of
them, just insert an empty one, except strand column, which can only
accept '1' '+' '-1' '-' and '*'.

You can download the develop version to accept a file name as inputs,
otherwise, you must feed the function an object of data.frame.

Yours sincerely,

Jianhong Ou

LRB 710
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605




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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