breakpointr {breakpointR} | R Documentation |
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 |
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 |
windowsize |
The window size used to calculate deltaWs, either number of reads or genomic size depending on |
binMethod |
Method used to calculate optimal number of reads in the window ("size", "reads"). By default |
multi.sizes |
User defined multiplications of the original window size. |
pairedEndReads |
Set to |
pair2frgm |
Set to |
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 |
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)