dot-readBam: Function to read in interaction-data stored in a BAM file

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

Function to read in interaction-data stored in a BAM file

Description

Reads in interactions stored in a BAM file. Assumes that each interaction is represented by pair of PETs with the same qname. The function reads in and determines which anchor is which by examining the isFirstMateRead and isSecondMateRead fields in the BAM file.

Usage

.readBam(fn)

Arguments

fn	name of BAM file containing interaction information

Value

list of GRanges - storing the anchor information for each interaction

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.