sig_convert: Convert Signatures between different Genomic Distribution of...

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Convert Signatures between different Genomic Distribution of Components

Description

Converts signatures between two representations relative to different sets of mutational opportunities. Currently, only SBS signature is supported.

Usage

sig_convert(sig, from = "human-genome", to = "human-exome")

Arguments

sig	a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix/data.frame with row representing components (motifs) and column representing signatures.
from	either one of "human-genome" and "human-exome" or an opportunity matrix (repeated n columns with each row represents the total number of mutations for a component, n is the number of signature).
to	same as from.

Details

The default opportunity matrix for "human-genome" and "human-exome" comes from COSMIC signature database v2 and v3.

Value

a matrix.

References

convert_signatures function from sigfit package.

Examples

# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Exome-relative to Genome-relative
sig_converted <- sig_convert(sig2,
  from = "human-exome",
  to = "human-genome"
)
sig_converted


show_sig_profile(sig2, style = "cosmic")
show_sig_profile(sig_converted, style = "cosmic")

ShixiangWang/sigminer documentation built on March 16, 2024, 12:30 p.m.