binOverFeature {ChIPpeakAnno} | R Documentation |
Aggregate peaks over bins from the feature sites.
binOverFeature(..., annotationData=GRanges(), select=c("all", "nearest"), radius=5000L, nbins=50L, minGeneLen=1L, aroundGene=FALSE, mbins=nbins, featureSite=c("FeatureStart", "FeatureEnd", "bothEnd"), PeakLocForDistance=c("all", "end","start","middle"), FUN=sum, errFun=sd, xlab, ylab, main)
... |
Objects of GRanges to be analyzed |
annotationData |
|
select |
Logical: annotate the peaks to all features or the nearest one |
radius |
The radius of the longest distance to feature site |
nbins |
The number of bins |
minGeneLen |
The minimal gene length |
aroundGene |
Logical: count peaks around features or a given site of the features. Default = FALSE |
mbins |
if aroundGene set as TRUE, the number of bins intra-feature. The value will be normalized by value * (radius/genelen) * (mbins/nbins) |
featureSite |
which site of features should be used for distance calculation |
PeakLocForDistance |
which site of peaks should be used for distance calculation |
FUN |
the function to be used for score calculation |
errFun |
the function to be used for errorbar calculation or values for the errorbar. |
xlab |
titles for each x axis |
ylab |
titles for each y axis |
main |
overall titles for each plot |
A data.frame with bin values.
Jianhong Ou
bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno") gr1 <- toGRanges(bed, format="BED", header=FALSE) data(TSS.human.GRCh37) binOverFeature(gr1, annotationData=TSS.human.GRCh37, radius=5000, nbins=10, FUN=length, errFun=0)