Firstly I'd like to thank the authors of the very useful package ChIPpeakAnno.
I'd like to report a feature in ChIPpeakAnno annotatePeakInBatch function
results that other users may or may not be aware of. I also propose
improvements to compensate.
The resulting insideFeature column reports TRUE if the query peak is either
contained within an annotated feature, and also reports TRUE if it overlaps the
end of an annotated feature.
I think its worth noting that it reports FALSE if the peak overlaps the
beginning of an annotated feature, and also reports FALSE if the peak overlaps
in entirety an annotated feature(s).
So, perhaps the insideFeature column (or additional new column called
overlappingFeature) could report five options:
("false","inside","overlapStart","overlapEnd","super"). I haven't looked into
the effects on how distanceToFeature should/could be called for each different
scenario.
Apologies if this has already been addressed, or if others do not consider this
useful.
Details with dummy example are described below.
Many thanks,
Amy.
#####
In the dummy example below, p1 is bigger than f1 and consequently p1 overlaps
it in entirety. It would be nice if ChIPpeakAnno could report this - although I
accept it may overlap more than one feature,
so would need to consider how to deal with that.
And another example from below, p3 in fact overlaps with the start of f3, but
is called as insideFeature=FALSE. It would be nice if ChIPpeakAnno could report
it as OverlapStart.
p4 is called as insideFeature = TRUE for overlapping with f4, but it would be
nice if ChIPpeakAnno could report it as OverlapEnd or something similar.
And correctly p2 is called as insideFeature = TRUE for overlap with f2, in this
case p2 ranges are within the f2 ranges as you would expect.
library(ChIPpeakAnno)
peaks =
RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,167889600),end=c(1555199,1560599,1565199,1573799,167893599),names=c("p1","p2","p3","p4","p5")),strand=as.integer(1),space=c(6,6,6,6,5))
features =
RangedData(IRanges(start=c(1549800,1554400,1565000,1569400,167888600),end=c(1550599,1560799,1565399,1571199,167888999),names=c("f1","f2","f3","f4","f5")),strand=as.integer(1),space=c(6,6,6,6,5))
annoPeaks = annotatePeakInBatch(peaks,AnnotationData=features)
as.data.frame(annoPeaks)
space start end width names strand feature start_position
1 5 167889600 167893599 4000 p5 1 f5 167888600
2 6 1543200 1555199 12000 p1 1 f1 1549800
3 6 1557200 1560599 3400 p2 1 f2 1554400
4 6 1563000 1565199 2200 p3 1 f3 1565000
5 6 1569800 1573799 4000 p4 1 f4 1569400
end_position insideFeature distancetoFeature
1 167888999 FALSE 1000
2 1550599 FALSE -6600
3 1560799 TRUE 2800
4 1565399 FALSE -2000
5 1571199 TRUE 400
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_1.3.0 org.Hs.eg.db_2.3.6
[3] GO.db_2.3.5 RSQLite_0.7-3
[5] DBI_0.2-4 AnnotationDbi_1.8.0
[7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.14.0
[9] Biostrings_2.14.2 IRanges_1.5.18
[11] multtest_2.2.0 Biobase_2.6.0
[13] biomaRt_2.3.0
loaded via a namespace (and not attached):
[1] MASS_7.3-3 RCurl_1.3-0 XML_2.6-0 splines_2.10.0
[5] survival_2.35-7
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