SMC_perPID: Run SMC at a per sample level

In YAPSA: Yet Another Package for Signature Analysis

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
 

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