Read CliP results

CliP is an algorithm for clonal structure identification through penalizing pairwise differences by Wenyi Wang Lab at MD Anderson Cancer Center in Houston.

Usage

read_clip_all(dir)

read_clip_all_wide(dir)

read_clip_best_lambda(dir)

Arguments

dir

directory in which to seek for the CliP results

Functions

• read_clip_all(): Read CliP results for all lambdas

• read_clip_all_wide(): Read CliP results for all lambdas, in the wider format

• read_clip_best_lambda(): Read CliP results for best lambda only

Examples

dir <- system.file("extdata", "CliP", package = "readthis")
read_clip_best_lambda(dir)
#> $mutation_assignments
#> # A tibble: 8,497 × 6
#>    sample_id chrom   pos cluster_index lambda best_lambda
#>    <chr>     <chr> <dbl>         <dbl> <chr>  <lgl>      
#>  1 SampleA   chr1      1             2 0.2    TRUE       
#>  2 SampleA   chr1      2             1 0.2    TRUE       
#>  3 SampleA   chr1      3             2 0.2    TRUE       
#>  4 SampleA   chr1      4             0 0.2    TRUE       
#>  5 SampleA   chr1      5             2 0.2    TRUE       
#>  6 SampleA   chr1      6             0 0.2    TRUE       
#>  7 SampleA   chr1      7             0 0.2    TRUE       
#>  8 SampleA   chr1      8             2 0.2    TRUE       
#>  9 SampleA   chr1      9             1 0.2    TRUE       
#> 10 SampleA   chr1     10             0 0.2    TRUE       
#> # ℹ 8,487 more rows
#> 
#> $subclonal_structure
#> # A tibble: 7 × 6
#>   sample_id cluster_index num_SNV cellular_prevalence lambda best_lambda
#>   <chr>             <dbl>   <dbl>               <dbl> <chr>  <lgl>      
#> 1 SampleA               0    1894              0.928  0.2    TRUE       
#> 2 SampleA               1     575              0.233  0.2    TRUE       
#> 3 SampleA               2    1817              0.0884 0.2    TRUE       
#> 4 SampleB               0    1903              0.968  0.1    TRUE       
#> 5 SampleB               1     238              0.49   0.1    TRUE       
#> 6 SampleB               2     558              0.230  0.1    TRUE       
#> 7 SampleB               3    1512              0.0867 0.1    TRUE       
#>