makeCpGregions: Cluster

In christpa/DMRScan: Detection of Differentially Methylated Regions

Cluster

Description

Cluster CpGs together in regions based on proximity

Usage

makeCpGregions(observations, chr, pos, maxGap = 500, minCpG = 2)

Arguments

observations	Vector of corresponding observed T-value for each CpG, must be ordered in the same way as chr and pos
chr	Vector of chromosome location for each CpG
pos	Vector giving base pair position for each CpG If unsorted, use order(chr,pos) to sort the genomic positions within each chromosome.
maxGap	Maximum allowed base pair gap within a cluster. Default is set to 500.
minCpG	Minimum number of CpGs allowed in each region to be considered. Default is set to at least 2 CpGs within each region.

Value

The suplied observations ordered into into a GRangesList object. To be parsed further into dmrscan

Examples

data(DMRScan.methylationData) ## Load methylation data from chromosome 22
data(DMRScan.phenotypes) ## Load phenotype (end-point for methylation data)

## Test for an association between phenotype and Methylation
testStatistics <- apply(DMRScan.methylationData,1,function(x,y)
 summary(glm(y ~ x, family = binomial(link = "logit")))$coefficients[2,3],
 y = DMRScan.phenotypes)

## Set chromosomal position to each test-statistic
pos<- data.frame(matrix(as.integer(unlist(strsplit(names(testStatistics),
split="chr|[.]"))), ncol = 3, byrow = TRUE))[,-1] 

## Set clustering features 
minCpG <- 3  ## Minimum number of CpGs in a tested cluster 
## Maxium distance (in base-pairs) within a cluster before it is 
## broken up into two seperate cluster
maxGap <- 750  
regions <- makeCpGregions(observations = testStatistics, chr = pos[,1], 
                            pos = pos[,2], maxGap = maxGap, minCpG = minCpG)

christpa/DMRScan documentation built on Feb. 2, 2024, 5:12 a.m.