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

Kcall_CpG

R Documentation

K-caller

Description

Employing preprocessing in combination with the algorithm dbscan, it allows the counting of clusters in the U/M plane. If plot = TRUE, a U/M plot is produced for which each cluster in coloured. Outliers, samples belonging to no cluster, will be coloured in black (as defined by the dbscan algorithm).

Usage

Kcall_CpG(CpG, M, U, plot = T, minPts = 12, eps = 0.035)

Arguments

`CpG`	Targeted CpG
`M`	Methylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
`U`	Unmethylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
`plot`	Logical. Whether to visualize the K-callers output in the U/M plane or not.
`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.

Details

Prior tuning of parameters eps, minPts is absolutely necessary and will depend on the sample size of the dataset employed. Parameters minPts = 12, eps = 0.05 were optimal in the E-risk cohort (n = 852). Smaller datasets will probably require reducing minPts and increasing eps, while larger datasets will probably require increasing minPts and reducing eps. For finding optimal parameters, are training set is available at UMtools; see help(training_set) for more details.