gintervals.load_chain: Loads assembly conversion table from a chain file

In misha: Toolkit for Analysis of Genomic Data

Loads assembly conversion table from a chain file

Description

Loads assembly conversion table from a chain file.

Usage

gintervals.load_chain(file = NULL)

Arguments

file	name of chain file

Details

This function reads a file in 'chain' format and returns assembly conversion table that can be used in 'gtrack.liftover' and 'gintervals.liftover'.

Note: chain file might map a few different source intervals into a single target one. These ambiguous mappings are not presented in the data frame returned by 'gintervals.load_chain'.

Value

A data frame representing assembly conversion table.

See Also

gintervals.liftover, gtrack.liftover

Examples

gdb.init_examples()
chainfile <- paste(.misha$GROOT, "data/test.chain", sep = "/")
gintervals.load_chain(chainfile)

misha documentation built on Sept. 14, 2023, 5:08 p.m.