paf2continuousScale: Define shift of genomic coordinates in order to get...

In daewoooo/SVbyEye: Visualization of genomic structural variants

Define shift of genomic coordinates in order to get continuous coordinate scale.

Description

This function takes a PAF alignments loaded by readPaf function and defines how much to shift genomic coordinates in order to get continuous coordinates in cases when there more than one query or target sequences in the input PAF alignments.

Usage

paf2continuousScale(paf.table)

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.

Value

A tibble of PAF alignments reported with a continuous coordinates.

Author(s)

David Porubsky

Examples

## Get PAF to plot
paf.file <- system.file("extdata", "test_ava.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Filter PAF
paf.table <- paf.table[paf.table$t.name == 'HG03453_2',]
## Define shift in genomic coordiantes to get continuous scale
paf2continuousScale(paf.table)

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