pafToBins: A wrapper function for 'pafAlignmentToBins' binning multiple...

In daewoooo/SVbyEye: Visualization of genomic structural variants

A wrapper function for pafAlignmentToBins binning multiple PAF alignments into a set of binned alignments between query and target sequence.

Description

A wrapper function for pafAlignmentToBins binning multiple PAF alignments into a set of binned alignments between query and target sequence.

Usage

pafToBins(paf.table = NULL, binsize = 10000)

Arguments

paf.table	A data.frame or tibble containing a single or multiple PAF record(s) with 12 mandatory columns along with CIGAR string defined in 'cg' column.
binsize	A size of a bin in base pairs to split a PAF alignment into.

Value

A list of tibble objects storing matched ('M') alignments as well as structurally variable ('SV') bases if 'report.sv' is TRUE.

Author(s)

David Porubsky

Examples

## Get PAF to bin ##
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Split multiple PAF alignments into user defined bins
pafToBins(paf.table = paf.table, binsize = 10000)

daewoooo/SVbyEye documentation built on March 31, 2024, 8:58 a.m.