decomposition: decomposition

In AlexandrovLab/SigProfilerExtractorR: Extracts Mutational Signatures from Cancer Genomes and Decompose the Signatures into Global Signatures

decomposition

Description

Decomposes the De Novo Signatures to Cosmic Signatures

Usage

decomposition(signatures, activities, samples, output,
  mutation_type = "96", genome_build = "GRCh37", verbose = F)

Arguments

signatures	A string. Path to a tab delimited file that contains the signaure table where the rows are mutation types and colunms are signature IDs.
activities	A string. Path to a tab delimilted file that contains the activity table where the rows are sample IDs and colunms are signature IDs.
samples	A string. Path to a tab delimilted file that contains the activity table where the rows are mutation types and colunms are sample IDs.
output	A string. Path to the output folder.
mutation_type	A string. The context type. Example: "96", "192", "1536", "6144", "INDEL", "DINUC". The default value is "96".
genome_build	A string. The genome type. Example: "GRCh37", "GRCh38", "mm9", "mm10". The default value is "GRCh37"
verbose	Boolean. Prints statements. Default value is False.

Value

A folder with decomposition results The files below will be generated in the output folder:

1.comparison_with_global_ID_signatures.csv
3.Decomposed_Solution_Samples_stats.txt
4.Decomposed_Solution_Signatures.txt
5.decomposition_logfile.txt
6.Mutation_Probabilities.txt
7.Signature_assaignment_logfile.txt
8.Signature_plot[MutatutionContext]_plots_Decomposed_Solution.pdf

AlexandrovLab/SigProfilerExtractorR documentation built on July 15, 2024, 12:08 p.m.