DMR {sesame} | R Documentation |
This subroutine uses Euclidean distance to group CpGs and then combine p-values for each segment. The function performs DML test first if cf is NULL. It groups the probe testing results into differential methylated regions in a coefficient table with additional columns designating the segment ID and statistical significance (P-value) testing the segment.
DMR( betas, cf, platform = NULL, refversion = NULL, dist.cutoff = NULL, seg.per.locus = 0.5 )
betas |
beta values for distance calculation |
cf |
coefficient table from DML or DMLShrinkage |
platform |
EPIC, HM450, MM285, ... |
refversion |
hg38, hg19, mm10, ... |
dist.cutoff |
distance cutoff (default to use dist.cutoff.quantile) |
seg.per.locus |
number of segments per locus higher value leads to more segments |
coefficient table with segment ID and segment P-value
sesameDataCache("HM450") # in case not done yet data <- sesameDataGet('HM450.76.TCGA.matched') cf_list = summaryExtractCfList(DML(data$betas, ~type, meta=data$sampleInfo)) cf_list = DMR(data$betas, cf_list$typeTumour)