detect_clonal_loh: Call clonal LOH using SNP density. Rcommended for cell lines...
In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq
detect_clonal_loh R Documentation
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)
numbat documentation built on May 29, 2024, 1:29 a.m.
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| detect_clonal_loh | R Documentation |
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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