R: Make a custom data structure for subgroups

make_subgroups_df {YAPSA}

R Documentation

Make a custom data structure for subgroups

Description

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.

Usage

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
)

Arguments

`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_vcf_like_df` carries the subgroup information
`in_PID.field`	String indicating which column of `in_vcf_like_df` and of `in_exposures_df` carries the PID information
`in_verbose`	Whether verbose or not.

Value

subgroups_df: A data frame carrying the subgroup and rank information.

Examples

 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)