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.

### See Also

`aggregate`

### 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)

[Package YAPSA version 1.20.1 Index]