Calculate the weights for the Row-Column-Exclusivity test

The weight for each mutation in the Row-Column-Exclusivity test cannot be calculated exactly for most use cases because there is no closed formula and a very large number of possible matrices to consider. Thus, the weights are calculated empirically from a sufficiently large number of samples of possible matrices.

calculate_row_col_exclusivity_weights(dat, sample_col, mutgene_col,
  Q = 100, quiet = TRUE)

Arguments

dat	tibble with mutation information
sample_col	column of samples names (quoted)
mutgene_col	column of genes that are mutated (quoted)
Q	number of permutation matrices to use (default is 100)
quiet	boolean for showing messages as run permutations (default is TRUE)

Examples

library(wext)
calculate_row_col_exclusivity_weights(dat = simple_dataset,
                                      sample_col = sample_name,
                                      mutgene_col = mutated_gene,
                                      Q = 5)
#> # A tibble: 72 x 3
#>    sample_name mutated_gene row_col_ex_weights
#>    <chr>       <chr>                     <dbl>
#>  1 1           a                           0.8
#>  2 1           b                           1  
#>  3 1           c                           0.8
#>  4 1           d                           1  
#>  5 1           e                           0.4
#>  6 1           g                           0.6
#>  7 1           h                           0.4
#>  8 10          a                           0.2
#>  9 10          b                           0.2
#> 10 10          c                           0.2
#> # … with 62 more rows