StandardChromNameNew: Standardize the chromosome name annotations for a data frame.

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Standardize the chromosome name annotations for a data frame.

Description

Standardize the chromosome name annotations for a data frame.

Usage

StandardChromNameNew(df, name.of.VCF = NULL)

Arguments

df	An in-memory data.frame representing a VCF.
name.of.VCF	Name of the VCF file.

Value

A list with the elements

• df a data frame with variants that had "legal" chromosome names (see below for illegal chromosome names).

• discarded.variants: Non-NULL only if there are variants with illegal chromosome names; these are names that contain the strings "GL", "KI", "random", "Hs", "M", "JH", "fix", "alt".

ICAMS documentation built on June 15, 2025, 1:08 a.m.