filterPaf: Filter PAF alignments.
In daewoooo/SVbyEye: Visualization of genomic structural variants

filterPaf

R Documentation

Filter PAF alignments.

Description

This function takes loaded PAF alignments using readPaf function and perform user defined filtering of input alignments based on mapping quality, alignment length, and minimum alignments between target and query.

Usage

filterPaf(
  paf.table,
  min.mapq = 10,
  min.align.len = 1000,
  min.align.n = 1,
  is.selfaln = FALSE,
  min.selfaln.dist = 0
)

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.
`min.mapq`	Minimum mapping quality to retain.
`min.align.len`	Minimum alignment length to retain.
`min.align.n`	Minimum number of alignments between a pair of sequences/regions.
`is.selfaln`	Set to `TRUE` if processing alignments of a given sequence to itself.
`min.selfaln.dist`	Keep alignment pairs with this or larger distance from each other (Applied only to FASTA self-alignments).

Value

A tibble of filtered PAF alignments.

Author(s)

David Porubsky

Examples

## Get PAF to plot
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")
## Filter PAF alignments based on desired target region
filterPaf(paf.table = paf.table, min.align.len = 50000)

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.