get_which: get_which

In shlienlab/ShlienLab.Core.Filter: ShlienLab.Core.Filter

Description

Function to calculate the 'which' parameter when loading a BAM file through Rsamtools. Given a chromosome and position, will calculate the appropriate access of the subset of data from the file, without loading unnecessary data.

Usage

get_which(chr = NULL, position = NULL, offsets = NULL)

Arguments

chr	String representing a chromosome (e.g. "X", "12") (required).
position	Integer representing the position in question, The function will return all the reads which overlap this position.
offsets	Positive integer dictating interval to the right of the position in which to access all reads from the BAM file (required).

Value

Produces a range that can be used to create a param object to open a subset of a BAM file in a separate function.

Author(s)

L. Christine Schreiner

shlienlab/ShlienLab.Core.Filter documentation built on May 20, 2019, 5:27 p.m.