SMC_perPID {YAPSA} | R Documentation

## Run SMC at a per sample level

### Description

Run an SMC analysis (stratification of the mutational catalogue) at per sample / per-PID level, corresponding to a divide and conquer strategy. For every single PID, only those signatures actually present in this PID will be provided for the SMC analysis.

### Usage

    SMC_perPID(
      in_dfList,
      in_LCDlist,
      in_subgroups_df,
      in_save_plot = TRUE,
      in_save_dir = NULL,
      in_save_name = "KataegisSMCs.pdf",
      in_verbose_flag = 0,
      ...
    )

### Arguments

`in_dfList` | Named list of vcf-like data frames, one entry per sample/PID of a cohort.
`in_LCDlist` | Output of an LCD list perfomed on the above cohort, carrying notably information on the exposures (`in_LCDlist$exposures`), the present signatures (`in_LCDlist$signatures`) and meta information about the signatures(`in_LCDlist$out_sig_ind_df`).
`in_subgroups_df` | Data frame with subgroup information about the PIDs in the above mentioned cohort.
`in_save_plot` | Boolean flag to indicate whether per-PID plots should be saved.
`in_save_dir` | If per-PID plots are to be saved, this is the path where to save them.
`in_save_name` | Suffix to be appended to the sample name to generate the name of the saved per-PID plots.
`in_verbose_flag` | Whether to run verbose (1) or not (0).
`...` | Data passed on to `run_SMC`.

### Value

A list of lists. The top level is a named per-PID list, each entry is of type SMClist (cf. `run_SMC`).

### Examples

     NULL

[Package YAPSA version 1.18.0 Index]