GetAggregateVPlot: Obtain the aggregate VPlot matrix over a set of chromosomal...

In jbelsky/TyphoonPlot: Creating Genomic Typhoon Plots

Description

Given a data frame listing chromosomal coordinates, an indexed bam file, and a bp window, this function will return a matrix displaying the paired-end, sequenced reads in a standard V-plot (e.g. at the midpoint-fragment length location in a matrix.

Usage

GetAggregateVPlot(data.df, bam_file_name, win)

Arguments

data.df	Data Frame, a feature data frame containing the "chr", "mid", and "strand" components for each location in the dataset
bam_file_name	Character, a bam file and its associated .bai index file
win	Numeric, number of bp to extend the V-plot from the midpoint location

Value

A frag_length x position matrix (250 rows x (2*win + 1) columns) that can be visualized with DensDotPlot

Examples

## Not run: GetAggregateVPlot(abf1_yeast_sacCer2.df, "/home/jab112/dm242.bam", 500)

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