clusterMaker: clusterMaker

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Description

clusterMaker function based on spatial distance

Usage

clusterMaker(chr, pos, maxGap = 500, names)

Arguments

chr	Chromosome vector
pos	position numeric vector
maxGap	max gap length between 2 probes within a region
names	probe names vector

Details

If you define the maxGap 500, so we can guarantee probes in different regions has distance >= maxGap. As the result, if we extend region upstream & downstream maxGap / 2, our extended regions have no overlap

Value

cluster data.frame of length m(m probes). Probes within same region have same region identities list.

Examples

require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
Location <- data.frame(IlluminaHumanMethylation450kanno.ilmn12.hg19@data$Locations)
Probes <- rownames(Location)[rownames(Location) %in% rownames(dat.m)]
BED <- cbind(Location[Probes, 1:2])
BED <- cbind(BED, dat.m[Probes, 4:3])
cluster <- clusterMaker(chr = BED$chr, pos = BED$pos, maxGap = 1000, names = rownames(BED))

xinchoubiology/Rcppsva documentation built on May 4, 2019, 1:06 p.m.