GetTyphoonPlotMat: Obtain the TyphoonPlot matrix needed for plotting.

In jbelsky/TyphoonPlot: Creating Genomic Typhoon Plots

Description

Given an indexed bam file and chromosomal genomic coordinates, this function will return a matrix displaying the paired-end, sequenced reads in two dimensions. Note that this function will plot reads at half their span to reduce the overlap between adjacent reads. For example, a 100 bp paired-end read spanning from position 201 to 300 will fill a 50 bp x-coordinate region from position 226 to 275.

Usage

GetTyphoonPlotMat(bam_file_name, chr, start_pos, end_pos)

Arguments

bam_file_name	Character, a bam file and its associated .bai index file
chr	Character, chromosome from the bam file
start_pos	Numeric, genomic start position
end_pos	Numeric, genomic end position

Value

A frag_length x position matrix (250 rows x position columns) that can be visualized with DensDotPlot

Examples

## Not run: GetTyphoonPlotMat("/home/jab112/dm242.bam", "1", 10000, 15000)

jbelsky/TyphoonPlot documentation built on May 18, 2019, 5:59 p.m.