testROH.numeric: Tests if a segment is in Run-of-Homozygosity (ROH)

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Tests if a segment is in Run-of-Homozygosity (ROH)

Description

Tests if a segment is in Run-of-Homozygosity (ROH).

Usage

## S3 method for class 'numeric'
testROH(muN, csN=NULL, betaN=NULL, minNbrOfSnps=1, delta=1/12, ..., verbose=FALSE)

Arguments

muN	An numeric vector of J genotype calls in {0,1/2,1} for AA, AB, and BB, respectively, and NA for non-polymorphic loci.
csN	(optional) A numeric vector of J genotype confidence scores. If NULL, ad hoc scores calculated from betaN are used.
betaN	(optional) A numeric vector of J matched normal BAFs in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.
minNbrOfSnps	Minimum number of SNPs required to test segment. If not tested, NA is returned.
delta	A double scalar specifying the maximum (weighted) proportion of heterozygous SNPs allowed in an ROH region.
...	Not used.
verbose	See Verbose.

Value

Returns a logical.

Author(s)

Pierre Neuvial, Henrik Bengtsson

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.