bamSummarise: summarise mapping observations from a BAM file

In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Description

This method will parse BAM file and summarise the mapping observations in a way that can be used for preparation of figures and confidence plots by the nanopoRe package. This is single threaded and DOES NOT require access to reference genome.

Usage

bamSummarise(bamFile, force = FALSE, blockSize = 50000L)

Arguments

bamFile	is the location to the BAM file to parse
force	logical value of whether analysis should be force recalculated
blockSize	the number of reads to process in chunks

Value

data.frame of per read summary observations

Examples

demoBam <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
bamSummary <- bamSummarise(demoBam, force=FALSE, blockSize=1000L)

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.