bamSummariseByChr: summarise mapping observations from a BAM file by chromosome

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

Description

This method will parse a 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

Usage

bamSummariseByChr(chrId,
    bamFile,
    force = FALSE,
    blockSize = 10000L,
    index=NULL
)

Arguments

chrId	is the chromosome to parse
bamFile	is the location to the BAM file to parse
force	logical value describing whether the analysis should be force recalculated
blockSize	the number of reads to process at the time as iterating through
index	path to the BAI index file - should be automatic in most cases

Value

data.frame of per read summary observations

Examples

# load reference genome
init()
referenceFasta <- system.file("extdata",
    "Escherichia_coli_complete_genome.fasta",
    package = "nanopoRe")
setReferenceGenome(referenceFasta)
# load reference BAM
demoBam <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
# Rsamtools::BamFile has problems in picking up packaged .bam.bai
# we will specify it here rather then automatic detection
demoBamIdx <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
bamSummariseByChr(chrId=getChromosomeIds()[1],
    bamFile=demoBam,
    blockSize=100L,
    index=demoBamIdx)

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