breakpointr: Main function for the 'breakpointR' package
In breakpointR: Find breakpoints in Strand-seq data

Description Usage Arguments Value Author(s) Examples

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.

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
)

`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.

NULL

David Porubsky, Aaron Taudt, Ashley Sanders

## 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)