importBams: Import BAM(s) and count reads

In daewoooo/SaaRclust: R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.

Description

Import aligned reads from a multiple BAM files and counts directional reads in specified genomic locations. Results are stored in a list of matrices with each element of a list representing counts for single BAM file.

Usage

importBams(bamfolder = bamfolder, chromosomes = NULL,
  bin.length = 1e+06)

Arguments

bamfolder	A folder where BAM files to be processed are stored.
chromosomes	If only a subset of the chromosomes should be binned, specify them here.
bin.length	A length of a bin to count reads in.
pairedEndReads	Set to TRUE if you have paired-end reads in your file.

Value

A list of matrices (columns: minus (W) and plus (C) counts; rows: genomic regions).

Author(s)

David Porubsky

daewoooo/SaaRclust documentation built on May 28, 2019, 7:50 p.m.