This file is not a valid BED file, but it *is* a valid BEDgraph file.  Load
it with:

peaks <- rtracklayer::import("[cut]/Mapped.bed", format = "bedGraph")

Michael



On Wed, Mar 27, 2013 at 9:01 AM, Ou, Jianhong <Jianhong.Ou@umassmed.edu>wrote:

> 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@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.
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor@r-project.org
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >Search the archives:
> >http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

