[BioC] Query on ChipPeakAnno: AnnotatePeakinBatch input

[Zhu, Lihua (Julie)]

Parthav,

Could you please send us the code snippets,  a test bed file and the
sessionInfo? Thanks!

Best regards,

Julie


On 12/3/13 9:43 AM, "Jailwala, Parthav (NIH/NCI) [C]"
<parthav.jailwala at nih.gov> wrote:

> Hi Julie,
> 
> I have a strand issue with using the AnnotatePeakinBatch function within the
> ChipPeakAnno package and am reaching out to you to see if you can help to
> figure out what is the issue.
> 
> I am trying to find the distance to the TSS , for a set of lincRNA. To do
> this, I am using my own BED file of the 'background' or Annotation. The BED
> file looks like this:
> 
> Y       597158  623056  Ddx3y   -
> Y       346986  365290  Eif2s3y +
> Y       2118049 2129045 Gm10256 +
> Y       2156899 2168120 Gm10352 +
> Y       1976249 1976584 Gm16501 -
> Y       2390390 2398856 Gm3376  +
> 
> As you can see, there is now header row for the column names as well as, the
> fifth column is the strand of the feature.
> 
> Now, when I run the command, in the output file, the 'Strand' column is always
> +ve (Always + eventhough the feature is on ­ve strand).
> 
> Here is a sample from the output file:
> 
> "","space","start","end","width","names","peak","strand","feature","start_posi
> tion","end_position","insid
> eFeature","distancetoFeature","shortestDistance","fromOverlappingOrNearest"
> "1","1",9708702,9782003,73302,"0001
> 23152","0001","+","23152",9708703,9738463,"includeFeature",-1,1,"Near
> estStart"
> "2","1",134088012,134153958,65947,"0002
> 22624","0002","+","22624",134088013,134153958,"overlapStart",-1,0
> ,"NearestStart"
> "3","1",171899539,172040632,141094,"0003
> 22283","0003","+","22283",171902439,172040632,"overlapStart",-29
> 00,0,"NearestStart"
> "4","1",195333431,195335997,2567,"0004
> 22164","0004","+","22164",195172540,195196491,"downstream",160891,
> 136940,"NearestStart"
> 
> 
> I will really appreciate if you can tell me what is wrong with my inputs.
> 
> Thanks
> Parthav Jailwala
> 
> Parthav Jailwala [Contractor]
> Bioinformatics Analyst, CCRIFX Bioinformatics Core
> 
> Advanced Biomedical Computing Center (ABCC)
> Information Systems Program
> Leidos Biomedical Research, Inc.
> (formerly SAIC-Frederick, Inc.)
> Frederick National Laboratory for Cancer Research (FNLCR)
> P. O. Box B, Frederick, MD 21702
> 
> Building 41-B620, NIH, Bethesda, MD
> E-mail: parthav.jailwala at nih.gov<mailto:parthav.jailwala at nih.gov>
> Bethesda: 301.451.3455
> Frederick: 301.846.5664
> Fax (Bethesda): 301.480.0391
> http://ccrifx.cancer.gov<http://ccrifx.cancer.gov/>
> 
> [cid:3573556C-D796-400A-A322-DCBDDD35455A]