liftRangesToAlignment: Function to lift coordinates to the alignment in PAF format.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Function to lift coordinates to the alignment in PAF format.

Description

Function to lift coordinates to the alignment in PAF format.

Usage

liftRangesToAlignment(paf.table, gr = NULL, direction = "query2target")

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.
gr	A GRanges-class object containing single or multiple ranges in query or target sequence coordinates.
direction	One of the possible, lift ranges from query to target 'query2target' or vice versa 'target2query'.

Value

A GRanges-class object with resized original set of ranges.

Author(s)

David Porubsky

Examples

## Define range(s) to lift
roi.gr <- as("chr17:46645907-46697277", "GRanges")
## Get PAF alignment to lift to
paf.file <- system.file("extdata", "test_lift1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Lift target range to query coordinates
liftRangesToAlignment(paf.table = paf.table, gr = roi.gr, direction = "target2query")

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