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

Source: R/utils.R
detect_clonal_loh.Rd

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)