bb_read_bam: Read Bam Files

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

Read Bam Files

Description

This function reads a single sorted, dedupliated paired end bam file and returns either a GRanges object or a GenomicAlignmentPairs object. The former requires much less memory but a the cost of retaining the outer boundaries of each read. If read 1 has start S1 and end E1 and read 2 has start S2 and end S2, the Granges object spans S1-E2.

Usage

bb_read_bam(
  sortedBam,
  genome = c("hg38", "danRer11"),
  return_type = c("GenomicAlignmentPairs", "GRanges")
)

Arguments

sortedBam	File path to the bam file to load.
genome	One of "hg38" or "danRer11". This is used to clean up the granges object if necessary.
return_type	Type of object to return. GRanges is smaller. GenomicAlignmentPairs retains read pair data.

Value

An object according to return_type.

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.