SMC_perPID: Run SMC at a per sample level

Description Usage Arguments Value Examples

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

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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

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slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.