Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.

Usage

detect_clonal_loh(bulk, t = 1e-05, snp_rate_loh = 5, min_depth = 0)

Arguments

bulk: dataframe Pseudobulk profile
t: numeric Transition probability
snp_rate_loh: numeric The assumed SNP density in clonal LOH regions
min_depth: integer Minimum coverage to filter SNPs

Value

dataframe LOH segments

Examples

segs_loh = detect_clonal_loh(bulk_example)
#> Warning: Returning more (or less) than 1 row per `summarise()` group was deprecated in
#> dplyr 1.1.0.
#> ℹ Please use `reframe()` instead.
#> ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()`
#>   always returns an ungrouped data frame and adjust accordingly.
#> ℹ The deprecated feature was likely used in the numbat package.
#>   Please report the issue to the authors.