read_coordinates: Read positions of simulated coordinates (regions or sites) in...

In bodkan/slimr: Parse, process and filter SLiM output files in R

Read positions of simulated coordinates (regions or sites) in their original coordinate system.

Description

SLiM simulates everything as part of a single continuous "chromosome". Therefore, matching simulated coordinates to their real coordinates requires their transposition into a 0-based continuous coordinate system. This function reads a table in a BED-like format that makes it possible to "reverse transpose" the simulated 0-based coordinates into their original form using the "transpose_sites" function.

Usage

read_coordinates(file)

Arguments

file	Path to a BED-like file. See the required format bellow.

Details

The coordinate file must be in a TSV format and must contain columns chrom, start, end, slim_start and slim_end.

Value

GRanges object.

See Also

admixr::transpose_coordinates

bodkan/slimr documentation built on Feb. 3, 2024, 3:39 p.m.