breakPaf: A wrapper function for 'breakPafAlignment' expanding multiple...

In daewoooo/SVbyEye: Visualization of genomic structural variants

A wrapper function for breakPafAlignment expanding multiple PAF alignments into a set of matching bases between query and target sequence.

Description

A wrapper function for breakPafAlignment expanding multiple PAF alignments into a set of matching bases between query and target sequence.

Usage

breakPaf(
  paf.table = NULL,
  min.deletion.size = 50,
  min.insertion.size = 50,
  collapse.mismatches = TRUE,
  report.sv = TRUE
)

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.deletion.size	A minimum size (in base pairs) of a deletion to be retained.
min.insertion.size	A minimum size (in base pairs) of an insertion to be retained.
collapse.mismatches	Set to TRUE if mismatches should be collapsed in order expand matched regions.
report.sv	Set to TRUE if to report also ranges of deleted and inserted bases.

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 break
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF alignment
paf.table <- readPaf(paf.file = paf.file)
## Break PAF alignment at indels of 20 bp and longer
breakPaf(paf.table = paf.table, min.deletion.size = 20, min.insertion.size = 20)

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