annotate_to_genomic_features: Annotate genomic regions to a list of genomic features

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Annotate genomic regions to a list of genomic features

Usage

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

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 list. This is used for constructing the column name of the annotation columns.
type	For each type of genomic features, 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 the names in the annotation columns. The column names are constructed as "$prefix_$name"
ignore_strand	whether ignore strand information
...	pass to countOverlaps or percentOverlaps

Details

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

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 = "#")

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.