methylKit (version 0.99.2)

getTargetAnnotationStats: Get the percentage of target features overlapping with annotation from annotationByFeature

Description

This function retrieves percentage/number of target features overlapping with annotation

Usage

getTargetAnnotationStats(x, percentage = TRUE, precedence = TRUE)
# S4 method for annotationByFeature
getTargetAnnotationStats(x, percentage = TRUE,
  precedence = TRUE)

Arguments

x

an annotationByFeature or an annotationByGenicParts object

percentage

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

precedence

TRUE|FALSE. If TRUE there will be a hierachy of annotation features when calculating numbers (with promoter>exon>intron precedence) That means if a feature overlaps with a promoter it will be counted as promoter overlapping only, or if it is overlapping with a an exon but not a promoter, it will be counted as exon overlapping only whether or not it overlaps with an intron.

Value

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

Examples

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

ann=annotateWithFeatureFlank(methylDiff.obj,cpg.obj$CpGi,cpg.obj$shores,
feature.name="CpGi",flank.name="Shores")
getTargetAnnotationStats(ann,percentage=TRUE,precedence=TRUE)

# }