getGenotype: Calculate genotype for a specific genomic region

View source: R/genotypeRegions.R

getGenotypeR Documentation

Calculate genotype for a specific genomic region

Description

Based on directional Strand-seq reads from a genomic region reports most likely genotype based on binomial probabilites of allowed strand states (WW, CC or WC).

Usage

getGenotype(gr, min.reads = 5, alpha = 0.05)

Arguments

gr

A GRanges-class object that contains directional Strand-seq reads.

min.reads

Minimal number of reads to pursue genotyping.

alpha

Estimated level of background in Strand-seq reads.

Value

A data.frame of binomial probabilities for a given counts of plus and minus reads for a single cell. (rows=reads/genomic segments, cols=strand states)

Author(s)

David Porubsky


daewoooo/primatR documentation built on Oct. 22, 2024, 9:41 p.m.