GetTyphoonPlotMat: Obtain the TyphoonPlot matrix needed for plotting.

Description Usage Arguments Value Examples

View source: R/create_typhoon_plot_functions.R

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

1
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

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

jbelsky/TyphoonPlot documentation built on June 5, 2017, 5:12 p.m.