Create a chromDict of percent methylation difference at all sites.

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..

chromDictMeth(mat, IDs, filter_thresh)

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

Value

Returns a list of data.tables for each chromosome, for faster analysis.

Examples

chromDictMethylDiff <- chromDictMeth(eigen, c("trt", "ctl"))
#> Removing low depth sites...
#> Calculating mean methylation differences...
#> Splitting by chromosome...