gtracks: Produce genomic tracks

In CharlesJB/GenomicTracks: Easily build genomic tracks

Description

This function extract the coverages of bam files and print them in track format. It is also possible to add custom annotation in the form of a list of GRanges or a GRangesList. A TxDb object can also be used to add the names of the genes in the selected region.

Usage

gtracks(region, bam_files, ranges = NULL, annotation = NULL, org = NULL)

Arguments

region	A GRanges representing the region to display.
bam_files	A list of bam filename. They must be indexed with samtools index (i.e.: if you have a bam file named bam_file.bam, you must also have a file named bam_file.bam.bai in the same directory). The names of the elements of the list will be used as names for the displayed tracks.
ranges	A list of GRanges or a GRangesList of custom annotations to add to the display. The names of the elements of the list/GRangesList will be used for the displayed tracks.
annotation	A TxDb object to use for annotation must be used org param.
org	The OrgDb object matching the annotation.

Value

A ggbio::Tracks object.

Examples

region <- GRanges("chr1", IRanges(34840000, 34860000))
bam_files <- get_demo_bam_files()[1]
names(bam_files) <- "align1_rep1"
gtracks(region = region, bam_files = bam_files)

CharlesJB/GenomicTracks documentation built on May 6, 2019, 9:58 a.m.