make_subgroups_df {YAPSA} | R Documentation |
Creates a data frame carrying the subgroup information and the order in which
the PIDs have to be displayed. Calls aggregate
on
in_vcf_like_df
.
make_subgroups_df( in_vcf_like_df, in_exposures_df = NULL, in_palette = NULL, in_subgroup.field = "SUBGROUP", in_PID.field = "PID", in_verbose = FALSE )
in_vcf_like_df |
vcf-like data frame with point mutation calls |
in_exposures_df |
Data frame with the signature exposures |
in_palette |
Palette for colour attribution to the subgroups if nun-NULL |
in_subgroup.field |
String indicating which column of
|
in_PID.field |
String indicating which column of |
in_verbose |
Whether verbose or not. |
subgroups_df: A data frame carrying the subgroup and rank information.
data(lymphoma_test) data(lymphoma_cohort_LCD_results) choice_ind <- (names(lymphoma_Nature2013_COSMIC_cutoff_exposures_df) %in% unique(lymphoma_test_df$PID)) lymphoma_test_exposures_df <- lymphoma_Nature2013_COSMIC_cutoff_exposures_df[,choice_ind] make_subgroups_df(lymphoma_test_df,lymphoma_test_exposures_df)