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

runBreakpointr

R Documentation

Find breakpoints in Strand-seq data

Description

Find breakpoints in Strand-seq data. See section Details on how breakpoints are located.

Usage

runBreakpointr(
  bamfile,
  ID = basename(bamfile),
  pairedEndReads = TRUE,
  chromosomes = NULL,
  windowsize = 1e+06,
  binMethod = "size",
  multi.sizes = NULL,
  trim = 10,
  peakTh = 0.33,
  zlim = 3.291,
  background = 0.05,
  min.mapq = 10,
  pair2frgm = FALSE,
  filtAlt = FALSE,
  genoT = "fisher",
  minReads = 20,
  maskRegions = NULL,
  conf = 0.99
)

Arguments

`bamfile`	A file with aligned reads in BAM format.
`ID`	A character string that will serve as identifier in downstream functions.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`chromosomes`	If only a subset of the chromosomes should be binned, specify them here.
`windowsize`	The window size used to calculate deltaWs, either number of reads or genomic size depending on `binMethod`.
`binMethod`	Method used to calculate optimal number of reads in the window ("size", "reads"). By default `binMethod='size'`.
`multi.sizes`	User defined multiplications of the original window size.
`trim`	The amount of outliers in deltaWs removed to calculate the stdev (10 will remove top 10% and bottom 10% of deltaWs).
`peakTh`	The treshold that the peak deltaWs must pass to be considered a breakpoint (e.g. 0.33 is 1/3 of max(deltaW)).
`zlim`	The number of stdev that the deltaW must pass the peakTh (ensures only significantly higher peaks are considered).
`background`	The percent (e.g. 0.05 = 5%) of background reads allowed for WW or CC genotype calls.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`pair2frgm`	Set to `TRUE` if every paired-end read should be merged into a single fragment.
`filtAlt`	Set to `TRUE` if you want to filter out alternative alignments defined in 'XA' tag.
`genoT`	A method ('fisher' or 'binom') to genotype regions defined by a set of breakpoints.
`minReads`	The minimal number of reads between two breaks required for genotyping.
`maskRegions`	List of regions to be excluded from the analysis in `GRanges-class` object.
`conf`	Desired confidence interval of localized breakpoints.

Details

Breakpoints are located in the following way:

calculate deltaWs chromosome-by-chromsome
localize breaks that pass zlim above the threshold
genotype both sides of breaks to confirm whether strand state changes
write a file of _reads, _deltaWs and _breaks in a chr fold -> can upload on to UCSC Genome browser
write a file for each index with all chromosomes included -> can upload on to UCSC Genome browser

Value

A BreakPoint object.

Author(s)

David Porubsky, Ashley Sanders, Aaron Taudt

Examples

## Get an example file
exampleFolder <- system.file("extdata", "example_bams", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Run breakpointR
brkpts <- runBreakpointr(exampleFile, chromosomes='chr22', pairedEndReads=FALSE)

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