Call DMRs from WGBS data.

DMR Calling.

Get_Novel_DMRs(ranks, nSeeds, chromDictObj, DMR_resolution, 
QueryLimit, minCpGs, minZ, perms)

Arguments

ranks

Rank data frame from getPCRanks.

nSeeds

Integer, number of input seeds for DMR expansion.

chromDictObj

chromDict() output. If null, chromDict() is run internally.

DMR_resolution

Automatic=NULL. Integer, number of bases to increase the DMR by with each expansion. If NULL, QueryLimit/25.

QueryLimit

Automatic=5000. Maximum DMR expansion size (bp)

minCpGs

Automatic=15. Minimum CpGs in a DMR region, regions with fewer CpGs will be discarded.

minZ

Automatic=1. Absolute Z score threshold for DMR calling; internal value. Not recommended to play with this setting.

perms

Automatic=1000. Number of permutations to use when defining the null distribution. Increasing this value largely influences computational time with minimal return

Value

Returns a data.frame of all novel DMRs.

Examples

ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)
DMRs <- Get_Novel_DMRs(ranks, 2940, minCpGs=10)
#> Splitting data by chromosome...
#> Bootstrapping background distributions for each chromosome...
#> Compressing nearby seeds... 
#> done! Collapsed 2940 seeds to 250 seeds!
#> 
#> Expanding DMRs from 250 seeds...
#> Trimming 135 DMRs...
#> done!