annotateWithFeatureFlank {genomation} | R Documentation |
Function to annotate a given GRanges object with promoter,exon,intron & intergenic values
annotateWithFeatureFlank(target, feature, flank, feature.name = NULL, flank.name = "flank", strand = FALSE, intersect.chr = FALSE) ## S4 method for signature 'GRanges,GRanges,GRanges' annotateWithFeatureFlank(target, feature, flank, feature.name = NULL, flank.name = "flank", strand = FALSE, 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) |
flank |
a granges object storing chromosome locations of the flanks of the feature |
feature.name |
string for the name of the feature |
flank.name |
string for the name of the flanks |
strand |
If set to TRUE, annotation features and target features will be overlapped based on strand (def:FAULT) |
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(cage) cpgi.flanks = getFlanks(cpgi) flank.annot = annotateWithFeatureFlank(cage, cpgi, cpgi.flanks)