CheckOvercompression: Check if DMR calling seed number is ovcompressed.

In PCBS: Principal Component BiSulfite

Check if DMR calling seed number is ovcompressed.

Description

Identifies if seed number to use for DMR calling causes overcompression.

Usage

CheckOvercompression(ranks, CpG_cutoff, values, max.dmr.size, return.plot)

Arguments

ranks	Rank data frame from getPCRanks.
CpG_cutoff	NULL or numeric. If NULL, seed numbers tested will be input of the values argument. If numeric, seed numbers tested will be CpG_cutoff*values argument. Recommended to us rankDist estimate if not null
values	Numeric vector, either seed numbers to test if CpG_cutoff=NULL or multipliers if CpG_cutoff is numeric
max.dmr.size	Automatic=5000. Maximum DMR expansion size in downstream analysis. Note: pipeline is optimized for 5000bp max DMR size, it is not recommended to play with this value.
return.plot	T/F, whether to return a plot or a numeric representing the best seed number for downstream analysis

Value

If return.plot=T, a grob plotting input seed number vs. compressed seed number is returned. Otherwise, a numeric is returned containing the largest tested input value without detectable overcompression.

Examples

ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)
CheckOvercompression(ranks, 980)

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