a data.frame or matrix that contains the locations of sample and control BAM
files, respectively, in columns. The file locations in a row represent a sample and its corresponding
control, which is used for calling peaks.
the path to the folder to which output should be written. The path can be
either absolute or relative.
the path to the folder with the helper files generated by
preCopywriteR(). The helper files include the bin, mappability,
GC-content, and blacklist, files in .bed format.
a BiocParallelParam instance (see
BiocParallel Bioconductor pacakage)
that determines the settings used for parallel computing. Please refer to the
vignette for more information.
optional; the path to the capture regions file, which should be in .bed
format. Overlapping bait regions should be reduced into single regions. If
included, statistics on the overlap of peaks called by MACS and the capture
regions will be provided.
optional; logical that indicates whether intermediary .bam, .bai and peak
regions files should be kept after the analysis is done. Defaults to FALSE.
## Not run:
# samples <- list.files(pattern = ".bam$", full.names = TRUE)
# ## Use the first .bam file as a control for every sample
# # controls <- samples[rep(1, length(samples))]
# ## Use every sample as its own control (i.e., peaks are called on sample itself)
# controls <- samples
# sample.control <- data.frame(samples, controls)
# CopywriteR(sample.control = sample.control, destination.folder =
# "/PATH/TO/DESTINATIONFOLDER/", reference.folder =
# "/PATH/TO/REFERENCEFOLDER", ncpu = nrow(sample.control),
# capture.regions.file <- "/PATH/TO/CAPTUREREGIONSFILE")
# ## End(Not run)