SMC: Stratification of a Mutational Catalogue

In YAPSA: Yet Another Package for Signature Analysis

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

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.

• exposures_strata_list: The list of s strata specific exposures Hi, all are numerical data frames with l rows and m columns, l being the number of signatures and m being the number of samples

• exposures_both_rel_df_list: A list of s strata specific cohortwide (i.e. averaged over cohort) normalized exposures

• this_subgroups_df: subgroups_df adjusted for plotting

• subgroup_ind: Index of the subgroups chosen and relevant for plotting.

• decomposition_method: String telling whether LCD or NMF was used, relevant only for handing over to plot_SMC.

See Also

run_SMC

plot_SMC

LCD_SMC

Examples

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