[Bioc-sig-seq] ChIPpeakAnno Error when Strand is * and geneEnd for FeatureLocForDistance

[Zhu, Lihua (Julie)]

Dario,

Please download the modified package in dev with version 1.7.2.

Sarah, I also added option geneEnd for FeatureLocForDistance in
annotatePeakInBatch function.

Best regards,

Julie


On 3/17/11 2:00 AM, "Dario Strbenac" <D.Strbenac at garvan.org.au> wrote:

> It has become standard for Bioconductor packages to use * to represent either
> strand. When I try to use annotatePeakInBatch with RangedData that has * in
> it, it fails. Could this be repaired ?
> 
> Minimal example :
> 
> library(ChIPpeakAnno)
> 
> peaksGR <- GRanges("chr1", IRanges(seq(100, 300, 100), width = 20))
> genesGR <- GRanges("chr1", IRanges(200, 500), '+')
> 
> peaksRD <- as(peaksGR, "RangedData")
> genesRD <- as(genesGR, "RangedData")
> 
> annotatePeakInBatch(peaksRD, AnnotationData = genesRD)
> 
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
> 
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