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

Description Usage Arguments Value Examples

View source: R/create_typhoon_plot_functions.R

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

1
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

1
## Not run: GetAggregateVPlot(abf1_yeast_sacCer2.df, "/home/jab112/dm242.bam", 500)

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