chromDictMeth: Create a chromDict of percent methylation difference at all sites.
Description
chromDicts are lists of keyed data.tables that enable very fast computing times. Much like the primary PCBS function chromDict() which makes a chromDict of all locus ranks, the chromDictMeth() function makes is a list of chromosome-specific data.tables containing percent methylation differences at all loci..
Usage
chromDictMeth(mat, IDs, filter_thresh)
Value
Returns a list of data.tables for each chromosome, for faster analysis.
Arguments
mat
data.frame object containing percent methylation and locus information for all sites, in the format of eigen
IDs
character vector of IDs containing the common names for compared conditions. E.g., for samples trt1 & trt2 vs. ctl1 & ctl2, IDs=c("trt1", "ctl")
filter_thresh
Integer, a coverage threshold for filtering, where CpG coverage of all samples must be larger than this value. Auto=50