genotype.binom: Assign states to any given region using binomial test.

View source: R/GenotypeBreaks.R

genotype.binomR Documentation

Assign states to any given region using binomial test.

Description

Assign states to any given region using binomial test.

Usage

genotype.binom(wReads, cReads, background = 0.05, minReads = 10, log = FALSE)

Arguments

wReads

Number of Watson reads.

cReads

Number of Crick reads.

background

The percent (e.g. 0.05 = 5%) of background reads allowed for WW or CC genotype calls.

minReads

The minimal number of reads between two breaks required for genotyping.

log

Set to TRUE if you want to calculate probability in log space.

Value

A list with the $bestFit and $pval.

Author(s)

David Porubsky

Examples

## Get Crick and Watson read counts
## Crick read count
cReads <- 30
## Watson read count
wReads <- 5  
genotype.binom(cReads = cReads, wReads = wReads, background = 0.05, minReads = 10, log = TRUE)


daewoooo/breakpointR documentation built on Aug. 4, 2022, 11:21 p.m.