genotype.fisher: Assign states to any given region using Fisher Exact Test.

In daewoooo/breakpointR: Find breakpoints in Strand-seq data

Assign states to any given region using Fisher Exact Test.

Description

Assign states to any given region using Fisher Exact Test.

Usage

genotype.fisher(cReads, wReads, roiReads, background = 0.05, minReads = 10)

Arguments

cReads	Number of Crick reads.
wReads	Number of Watson reads.
roiReads	Total number of Crick and Watson 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.

Value

A list with the $bestFit and $pval.

Author(s)

David Porubsky, Aaron Taudt

Examples

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

daewoooo/breakpointR documentation built on April 20, 2023, 4:13 p.m.