| CheckOvercompression {PCBS} | R Documentation |
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)