annotate_to_genomic_features: Annotate to genomic features

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Annotate to genomic features

Usage

annotate_to_genomic_features(gr, genomic_features,
    name = NULL, type = c("percent", "number"), prefix = "overlap_to_", ...)

Arguments

gr	a GRanges object
genomic_features	a single GRanges object or a list of GRanges objects
name	names for the genomic features if there is no name in genomic_features
type	How to calculate the values for the annotation. number means numbers of genomic features that each region in gr overlap; percent means the percent of each region in gr that is overlapped by genomic features
prefix	prefix for names of the annotation columns
...	pass to countOverlaps or percentOverlaps

Details

It adds new columns in gr which tell you how gr is overlaped by genomic_features.

Note for the annotation, strand information is ignored.

Value

A GRanges with additional columns of annotations.

Author(s)

Zuguang Gu <[e-mail]>

Examples

require(circlize)
df1 = generateRandomBed(nr = 1000)
df2 = generateRandomBed(nr = 1000)
df3 = generateRandomBed(nr = 1000)
gr1 = GRanges(seqnames = df1[[1]], ranges = IRanges(df1[[2]], df1[[3]]))
gr2 = GRanges(seqnames = df2[[1]], ranges = IRanges(df2[[2]], df2[[3]]))
gr3 = GRanges(seqnames = df3[[1]], ranges = IRanges(df3[[2]], df3[[3]]))
annotate_to_genomic_features(gr1, list(gr2 = gr2, gr3 = gr3))
annotate_to_genomic_features(gr1, list(gr2 = gr2, gr3 = gr3), type = "number", prefix = "#")

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.