pileup: Calculate pileup for a BAM file.

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

Calculate pileup for a BAM file.

Usage

reads(x, ...)

reads(x) <- value

readfile(x, ...)

readfile(x) <- value

indelRate(x, ...)

indelRate(x) <- value

pileup(bamfile, reffile, readtype, ..., pParam)

Arguments

...	Additional parameters passed to PileupParam.
bamfile	<character>; path to bamfile.
reffile	<character>; Path to reference.
readtype	<character>; one of "illumina", "pacbio", or "nanopore".
pParam	A PileupParam object.

Details

Returns a pileup object: A list with slots:

bamfile

<character>; Path to the bamfile used to construct the pileup

reffile

<character>; Path to the reference used to construct the bamfile

refname

<character>; Name of the reference

readtype

<character>; One of "illumina", "pacbio", or "nanopore"

param

A PileupParam object

pilup

A tbl_df with colums:

seqnames

<character>; The RNAME field

pos

<integer>; Genomic position of base

nucleotide

<character>; Base

count

<integer>; Count of base

consmat

<consmat>; The consensus matrix

reads

<character>; (optional) names of n top-scoring reads

stats

<list>; Run statistics

Value

A pileup object. See Details.

Examples

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DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.