bamSummaryToCoverage: get depth of coverage information from across the genome

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

Description

This method will return a tiled Granges object containing mean depth of coverage information

Usage

bamSummaryToCoverage(bamFile=NULL,
    tilewidth = 1e+05,
    blocksize = 10000,
    flag = 'Primary',
    ...
)

Arguments

bamFile	- path to the bamFile to use
tilewidth	- the size of the window to use for the tiling
blocksize	to use for parsing the BAM file
flag	mapping type for filter (Primary/Secondary/Supplementary)
...	such as FORCE=TRUE

Value

GRanges object with mean depth of coverage data in binned_cov field

Examples

demoBam <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
referenceFasta <- system.file("extdata",
    "Escherichia_coli_complete_genome.fasta",
    package = "nanopoRe")
setReferenceGenome(referenceFasta)
bamSummarise(demoBam, blockSize=1000L)
bamSummaryToCoverage()

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