SMC_perPID {YAPSA} | R Documentation |
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.
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, ... )
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_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 |
A list of lists. The top level is a named per-PID list, each entry is
of type SMClist (cf. run_SMC
).
NULL