methylKit (version 0.9.5)

getFeatsWithTargetsStats: Get the percentage/count of annotation features overlapping with target features

Description

This function retrieves percentage/number of annotation features overlapping with targets. For example, if annotationByFeature object is containing statistics of differentially methylated regions overlapping with gene annotation. This function will return number/percentage of introns,exons and promoters overlapping with differentially methylated regions.

Usage

getFeatsWithTargetsStats(x,percentage=TRUE)

Arguments

x

an annotationByFeature or an annotationByGenicParts object

percentage

TRUE|FALSE. If TRUE percentage of annotation features will be returned. If FALSE, number of annotation features will be returned

Value

a vector of percentages or counts showing quantity of annotation features overlapping with target features

Examples

# NOT RUN {
data(methylKit)
cpg.obj=read.feature.flank(system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit"),feature.flank.name=c("CpGi","shores"))

ann=annotate.WithFeature.Flank(methylDiff.obj,cpg.obj$CpGi,cpg.obj$shores,feature.name="CpGi",flank.name="Shores")
getFeatsWithTargetsStats(ann,percentage=TRUE)
# }