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

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.