breakpointr: Main function for the 'breakpointR' package

View source: R/breakpointr.R

breakpointrR Documentation

Main function for the breakpointR package

Description

This function is an easy-to-use wrapper to find breakpoints with runBreakpointr in parallel, write the results to file, plot results and find hotspots.

Usage

breakpointr(
  inputfolder,
  outputfolder,
  configfile = NULL,
  numCPU = 1,
  reuse.existing.files = FALSE,
  windowsize = 1e+06,
  binMethod = "size",
  multi.sizes = NULL,
  pairedEndReads = FALSE,
  pair2frgm = FALSE,
  chromosomes = NULL,
  min.mapq = 10,
  filtAlt = FALSE,
  genoT = "fisher",
  trim = 10,
  peakTh = 0.33,
  zlim = 3.291,
  background = 0.05,
  minReads = 10,
  maskRegions = NULL,
  callHotSpots = FALSE,
  conf = 0.99
)

Arguments

inputfolder

Folder with BAM files.

outputfolder

Folder to output the results. If it does not exist it will be created.

configfile

A file specifying the parameters of this function (without inputfolder, outputfolder and configfile). Having the parameters in a file can be handy if many samples with the same parameter settings are to be run. If a configfile is specified, it will take priority over the command line parameters.

numCPU

The numbers of CPUs that are used. Should not be more than available on your machine.

reuse.existing.files

A logical indicating whether or not existing files in outputfolder should be reused.

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.

pairedEndReads

Set to TRUE if you have paired-end reads in your file.

pair2frgm

Set to TRUE if every paired-end read should be merged into a single fragment.

chromosomes

If only a subset of the chromosomes should be binned, specify them here.

min.mapq

Minimum mapping quality when importing from BAM files.

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.

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.

minReads

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

maskRegions

List of regions to be excluded from the analysis (tab-separated file: chromosomes start end).

callHotSpots

Search for regions of high abundance of breakpoints in single cells.

conf

Desired confidence interval of localized breakpoints.

Value

NULL

Author(s)

David Porubsky, Aaron Taudt, Ashley Sanders

Examples

## Not run: 
## The following call produces plots and genome browser files for all BAM files in "my-data-folder"
breakpointr(inputfolder="my-data-folder", outputfolder="my-output-folder")
## End(Not run)


daewoooo/breakpointR documentation built on May 9, 2024, 5:03 p.m.