create_indel_mut_cat_from_df: Create a Mutational catalog from a data frame

In YAPSA: Yet Another Package for Signature Analysis

Description

This function creates a mutational catalog from a data frame. It requires the returend data frame optainted with attribution_of_indels.

Usage

create_indel_mut_cat_from_df(in_df, in_signatures_df)

Arguments

in_df

A data frame constucted from a vcf-like file of a whole cohort or single-sample. The first coloums are those of a standart vcf file, followed by an arbitrary number of customs or used defined columns. One if these can carry a PID (patient or sample identefyier) and the subgroup information. Additionaly to consuct the the mutational catalog each variant needs to be characterize into one of the 83 INDEL feature classes, which can be perfomed with attribution_of_indels

in_signatures_df

A numeric data frame W with n rows and l columns, n being the number of features and l being the number of signatures.Data frame containing INDEL signatures which should be used to create the mutational cataolog V.

Value

A count dataframe, the mutational catalog V with rownames indicating the INDELs and colnames having the PIDs

Examples

data(GenomeOfNl_raw)
data(sigs_pcawg)
GenomeOfNl_context <- attribute_sequence_contex_indel(in_dat =
 head(GenomeOfNl_raw))
GenomeOfNl_classified <- attribution_of_indels(GenomeOfNl_context)
GenomeOfNl_mut_cat <- create_indel_mut_cat_from_df(GenomeOfNl_classified,
 in_signatures_df=PCAWG_SP_ID_sigs_df)

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.