[BioC] Help on ChIPpeakAnno

[Zhu, Lihua (Julie)]

Prashantha,

I was able to reproduce the intended distances from your example.
library(ChIPpeakAnno)
data(TSS.human.GRCh37)
myexp =  RangedData(IRanges(start=c(128391471), en=c(128391952),
names=c("p1")), strand=as.integer(1),space=c("11"))
annotatedPeak1= annotatePeakInBatch(myexp, AnnotationData =
TSS.human.GRCh37)
annotatedPeak1 

 space                 ranges |        peak      strand         feature

 11 [128391471, 128391952] |          p1           - ENSG00000134954
            start_position end_position insideFeature distancetoFeature
shortestDistance
       
      128328656    128457453        inside             65982
62815
                

Here is how the distancetoFeature is calculated. Please note that this is
the start position of the peak minus the TSS position (feature end if
feature is on - strand and feature start if feature is on + strand). If
feature is on - strand, reverse the sign of the distance. The confusion
might be due to that this feature is on the - strand.
> -(128391471 - 128457453)
[1] 65982

Here is the shortest distance
> min(abs(128391471 - 128328656), abs(128391471 - 128457453), abs(128391952 -
128328656), abs(128391952-128457453))
[1] 62815

Best regards,

Julie

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ChIPpeakAnno_1.6.0                  limma_3.6.9
 [3] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
 [5] RSQLite_0.9-4                       DBI_0.2-5
 [7] AnnotationDbi_1.12.0                BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.18.2                     GenomicRanges_1.2.2
[11] Biostrings_2.18.2                   IRanges_1.8.8
[13] multtest_2.6.0                      Biobase_2.10.0
[15] biomaRt_2.6.0 

loaded via a namespace (and not attached):
[1] MASS_7.3-9      RCurl_1.4-3     splines_2.12.1  survival_2.36-2
tools_2.12.1   
[6] XML_3.2-0  



On 3/9/11 3:33 AM, "Prashantha Hebbar" <prashantha.hebbar at yahoo.com> wrote:

> Dear all,
> 
> I have few issues with TSS information obtained through ChIPpeakAnno. To
> catalog 
> TSS information pertaining to my probe sets I have used TSS.human.GRCh37
> (ensemble) build. After obtaining information, data in the columns
> distanceToFeature and shorstestDistance do not exactly match with either
> SwitchGear TSS prediction available through UCSC or Eponine tss prediction
> available through Ensemble.
> 
> 
> Here is one such example I have encountered.
> To coordinate chr11:128391471-128391952, ChIPpeakAnno gave distanceToFeature
> as 
> 65982 and shorstestDistance as 62815. The given coordinate is from
> chr11:128328656-128457453 (ETS1). if we search with same coordinate in either
> UCSChg19(SwitchGear) or Ensemble (Eponine), for TSS, tss situates at 128392173
> position. if we subtract 128392173-128328656=63517. This in contradiction not
> matching to the ChIPpeakAnno (65982).
> 
> Can anybody please clarify this issue? How come with same build this
> difference? 
> 
> 
> Thanking you in anticipation.
> 
> Regards,
> Prashantha
> 
> Manipal Life Sciences Center,
> Manipal University,
> Manipal, India
> PIN: 576104
> Email:prashantha.hebbar at manipal.edu
> 
> 
>       
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> 
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