countProb: Calculate probability of PacBio reads having WW, CC or WC...

In daewoooo/SaaRclust: R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.

Description

Import counts of directional Strand-seq reads aligned to PacBio reads and calculates binomial probabilites of PacBio reads being WW, CC or WC state.

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/SaaRclust documentation built on May 28, 2019, 7:50 p.m.