annotateWithFeature {genomation} | R Documentation |
Function to annotate given GRanges object with a given genomic feature
annotateWithFeature(target, feature, strand = FALSE, extend = 0, feature.name = NULL, intersect.chr = FALSE) ## S4 method for signature 'GRanges,GRanges' annotateWithFeature(target, feature, strand = FALSE, extend = 0, feature.name = NULL, intersect.chr = FALSE)
target |
a GRanges object storing chromosome locations to be annotated |
feature |
a GRanges object storing chromosome locations of a feature (can be CpG islands, ChIP-seq peaks, etc) |
strand |
If set to TRUE, annotation features and target features will be overlapped based on strand (def:FAULT) |
extend |
specifiying a positive value will extend the feature on both
sides as much as |
feature.name |
name of the annotation feature. For example: H3K4me1,CpGisland etc. by default the name is taken from the given variable |
intersect.chr |
boolean, whether to select only chromosomes that are common to feature and target. FALSE by default |
returns an AnnotationByFeature
object
data(cpgi) data(promoters) annot = annotateWithFeature(cpgi, promoters)