genotyping {breakpointR}R Documentation

Set of functions to genotype regions in between localized breakpoints

Description

Each defined region is given one of the three states ('ww', 'cc' or 'wc') Consecutive regions with the same state are collapsed

Usage

GenotypeBreaks(breaks, fragments, background = 0.05, minReads = 10,
  genoT = "fisher")

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

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

Arguments

breaks

A GRanges-class object with breakpoint coordinates.

fragments

A GRanges-class object with read fragments.

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.

genoT

A method ('fisher' or 'binom') to genotype regions defined by a set of breakpoints.

cReads

Number of Crick reads.

wReads

Number of Watson reads.

roiReads

Total number of Crick and Watson reads.

log

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

Details

Function GenotypeBreaks exports states of each region defined by breakpoints. Function genotype.fisher assigns states to each region based on expected counts of Watson and Crick reads. Function genotype.binom assigns states to each region based on expected counts of Watson and Crick reads.

Value

A GRanges-class object with genotyped breakpoint coordinates.

A list with the $bestFit and $pval.

A list with the $bestFit and $pval.

Functions

Author(s)

David Porubsky, Ashley Sanders, Aaron Taudt

David Porubsky, Aaron Taudt

David Porubsky

Examples

## Get an example file 
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file 
breakpoint.objects <- get(load(exampleFile))
## Genotype regions between breakpoints
gbreaks <- GenotypeBreaks(breaks=breakpoint.objects$breaks, fragments=breakpoint.objects$fragments)


[Package breakpointR version 1.6.0 Index]