SMC {YAPSA} | R Documentation |
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
.
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 )
df_list |
A list of |
this_signatures_df |
A numeric data frame |
in_all_exposures_df |
The overall exposures |
number_of_strata |
The length of the 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 |
cohort_method_flag |
Either or several of
|
in_verbose |
Verbose if |
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
.
NULL