SMC: Stratification of a Mutational Catalogue
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Arguments Value See Also Examples

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.

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
)

`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`

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.