countProb: Calculate probability of a genomic region having WW, CC or WC...

View source: R/genotypeRegions.R

countProbR Documentation

Calculate probability of a genomic region having WW, CC or WC state.

Description

Exports most likely strand state (WW, CC or WC) based on counts of plus and minus reads and allowed level of background 'alpha'.

Usage

countProb(minusCounts, plusCounts, alpha = 0.1, log = FALSE)

Arguments

minusCounts

Minus (Watson) read counts aligned to PacBio reads.

plusCounts

Plus (Crick) read counts aligned to PacBio reads.

alpha

Estimated level of background in Strand-seq reads.

Value

A matrix 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, Maryam Ghareghani


daewoooo/primatR documentation built on March 28, 2024, 6:41 a.m.