eval_regions.RdEvaluate and annotate a given region to patient association data set
eval_regions(reg_to_patient_mut)A data.frame like object from panel_to_patient()
with all regions reg_id linked to patients patient_id via mutations mut_id.
It should additionally contain the following columns:
reg_chr
reg_start one-based
reg_end one-based
A data frame with all unique regions and additional annotations.
r2p <- panel_to_patient(gr_toy, mut_toy)
r2p
#> # A tibble: 6 × 10
#> reg_id reg_chr reg_start reg_end mut_id patient_id chr start end gene
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 r1 1 1 2 m01 p1 1 1000 1000 g1
#> 2 r1 1 1 2 m01 p2 1 1000 1000 g1
#> 3 r1 1 1 2 m01 p1 1 1000 1000 g1
#> 4 r1 1 1 2 m01 p2 1 1000 1000 g1
#> 5 r3 2 1 1 m03 p1 2 3000 3000 g2
#> 6 NA NA NA NA NA p3 NA NA NA NA
eval_regions(r2p)
#> # A tibble: 2 × 15
#> reg_id reg_chr reg_start reg_end n_region reg_size reg_size_cum n_patient
#> <chr> <chr> <dbl> <dbl> <int> <dbl> <dbl> <int>
#> 1 r1 1 1 2 1 2 2 2
#> 2 r3 2 1 1 2 1 3 1
#> # ℹ 7 more variables: n_patients_cum <dbl>, total_patients <int>,
#> # percent_patients <dbl>, percent_patients_cum <dbl>, n_patient_gain <dbl>,
#> # n_mut <int>, n_mut_cum <dbl>