detect_clonal_loh {numbat}

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

Description

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)