ICAMS: StandardChromNameNew – R documentation

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StandardChromNameNew

Standardize the chromosome name annotations for a data frame.

Standardize the chromosome name annotations for a data frame.

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

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

A list with the elements

df a data frame with variants that had "legal" chromosome names (see below for illegal chromosome names). Leading "chr" strings are removed.
discarded.variants: Non-NULL only if there variants with illegal chromosome names; these are names that contain the strings "GL", "Hs", "KI", "M", "random".

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

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release