reportPrepro: Summary plots of data preprocessed in bins by iDPT
In jeffbhasin/dptviz: dptviz

iDPT performs a preprocessing stage to convert a set of alignments in a BAM file to average coverage values in windows of a user-specified size genome-wide. This function saves a PDF file containing plots that summarize the distribution of these average coverage values and their relationship to CpG density on a specified reference genome.

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  reportPrepro(dptpath,
    chrs = c(sapply(seq(1, 22), function(x) paste("chr", x, sep = "")), "chrX", "chrY"),
    bsgenome, file = NULL, ncore = 1)

`dptpath`	Path to a folder containing an iDPT run (the folder than contains the "DPT_ws" folder)
`chrs`	A vector of chromosome names to use (by default, the autosomes and sex chromosomes from hg19)
`bsgenome`	A BSgenome object for the reference genome used in the alignments contained in the input BAM files given to iDPT (i.e. for UCSC's hg19, you would load "library(BSgenome.Hsapiens.UCSC.hg19)" and give BSgenome.Hsapiens.UCSC.hg19 to this argument). This is needed to compute CpG density in the windows used by iDPT.
`file`	Filename to save the PDF report to (if NULL, will use the name of the folder as a prefix and save "prefix.reportPrepro.pdf" in the current working directory")
`ncore`	Number of concurrent threads to use