getRegionScores {PCBS} | R Documentation |
Calculated methylation significance in a set of regions.
Description
Returns p-values and Z-scores for CpGs in a set of regions, compared to a local null background distribution.
Usage
getRegionScores(ranks, regions)
Arguments
ranks |
getPCRanks output data.frame |
regions |
A three-column dataframe containing a set of regions to test. Columns = chrom, start, end. |
Value
Returns a data.frame
with significance scores for all input regions.
Examples
ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)
DMLs <- addRanks(ranks)
# data.frame of regions to test:
regions <- data.frame(chr=c("chr3", "chr3", "chr1"),
s=c(4920450, 3961576, 300000),
e=c(4923267, 3963805, 302900),
ID=c("Hypo-DMR", "partial Hyper-DMR", "random"))
getRegionScores(DMLs, regions)
[Package PCBS version 0.1.0 Index]