par_EW_Kcalling: Epigenome-wide K-calling

In BenjaminPlanterose/UMtools: An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level

Epigenome-wide K-calling

Description

Same as Kcall_CpG but it performs K-calling on all the CpGs (rows) of a given matrix. Also, it allows parallel processing. If nThread is not specified, it will automatically detect how many clusters are available in the machine and will use N-1 cores.

Usage

par_EW_Kcalling(M, U, minPts = 12, eps = 0.035, nThread = NULL)

Arguments

M	Methylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
U	Unmethylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
minPts	dbscan parameter. Minimum numbers of points in the eps region to consider a core point; help(dbscan, dbscan) for more details.
eps	dbscan parameter. Size of the neighbourhood; help(dbscan, dbscan) for more details.
nThread	Number of CPU cores to employ

Value

Vector. Predicted number of clusters for each CpG.

Examples

annotation <- getAnnotation(rgSet)
chrY = rownames(annotation)[annotation$chr == "chrY"]
K_vec = par_EW_Kcalling(M[chrY,], U[chrY,])

BenjaminPlanterose/UMtools documentation built on Aug. 19, 2024, 4:54 a.m.