SMC: Stratification of a Mutational Catalogue

Description Usage Arguments Value See Also Examples

View source: R/SMC.R

Description

SMC takes a given collection of stratified mutational catalogues Vi, sends them to perform a mutational signatures decomposition by Linear Combination Decomposition (LCD) with the functions LCD_SMC with known signatures W. It subsequently performs some useful statistics and preparation for plotting with the function plot_SMC. SMC is naturally called by run_SMC.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
SMC(
  df_list,
  this_signatures_df,
  in_all_exposures_df,
  number_of_strata,
  number_of_sigs,
  name_list,
  this_subgroups_df,
  mutation_catalogue_all_df,
  cohort_method_flag,
  in_verbose = 1
)

Arguments

df_list

A list of s stratified mutational catalogues Vi \(numeric data frames\) with n rows and m columns each, n being the number of features and m being the number of samples.This list is naturally provided in run_SMC.

this_signatures_df

A numeric data frame W in with n rows and l columns, n being the number of features and l being the number of signatures

in_all_exposures_df

The overall exposures H without stratification, a numeric data frame with l rows and m columns, l being the number of signatures and m being the number of samples

number_of_strata

The length of the list df_list

number_of_sigs

The number of signatures used in the current decomposition.

name_list

A list of names of the different strata

this_subgroups_df

A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup

mutation_catalogue_all_df

The overall mutational catalogue V without stratification.

cohort_method_flag

Either or several of c("all_PIDs","cohort","norm_PIDs"), representing alternative ways to average over the cohort.

in_verbose

Verbose if in_verbose=1

Value

A list with entries exposures_strata_list, exposures_both_rel_df_list, this_subgroups_df, subgroup_ind and decomposition_method.

See Also

run_SMC

plot_SMC

LCD_SMC

Examples

1

slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.