SMC {YAPSA} | R Documentation

## Stratification of a Mutational Catalogue

### 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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[Package YAPSA version 1.18.0 Index]