classifiedAnnotationTrack: Get Classified Motif Annotation Track

Description Usage Arguments Value Examples

View source: R/annotation_visualize.R

Description

This function returns an annotated GeneRegionTrack that can be plotted alone or layered with other Gvix/ggbio tracks.

Usage

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classifiedAnnotationTrack(motif_bed, gen, thresh = 0)

Arguments

motif_bed

A string of the full path to the BED file containing the classified motifs

gen

A named character containing the chromosome name

thresh

An optional numeric value denoting the threshold of significance. Motifs with membership scores greater than or equal to thresh will be returned.

Value

A Formal Class GeneRegionTrack for enriched motif with GRanges corresponding to motif's genomic ranges,

Examples

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## Not run: 
data("A549ChromLoops")
data("matchedMotifs")
classify(matchedMotifs, A549ChromLoops)
gen <- c("mm10")
names(gen) <- "chr18"
antrack <- classifiedAnnotationTrack("./BEDs/H3K9me3.bed", gen)

## End(Not run)

NElnour/annotator3D documentation built on Dec. 8, 2019, 9:22 a.m.