deltaWCalculator: Calculate deltaWs

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

Calculate deltaWs

Description

This function will calculate deltaWs from a GRanges-class object with read fragments.

Usage

deltaWCalculator(frags, reads.per.window = 100)

Arguments

frags	A GRanges-class with read fragments (see readBamFileAsGRanges).
reads.per.window	Number of reads in each dynamic window.

Value

The input frags with additional meta-data columns.

Author(s)

Aaron Taudt

See Also

readBamFileAsGRanges

Examples

## Get an example file
exampleFolder <- system.file("extdata", "example_bams", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file
fragments <- readBamFileAsGRanges(exampleFile, pairedEndReads=FALSE, chromosomes='chr22')
## Calculate deltaW values
dw <- deltaWCalculator(fragments)

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