getGenotype: Calculate genotype for a specific genomic region

In daewoooo/primatR: What the Package Does (TODO)

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 March 28, 2024, 6:41 a.m.