chromDictMeth: Create a chromDict of percent methylation difference at all...

In PCBS: Principal Component BiSulfite

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)

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"))

PCBS documentation built on Sept. 11, 2024, 6:11 p.m.