CandidateDMRFinder.v2: CandidateDMRFinder.v2
In immunomethylomics/IDOL: IDentifying Optimal DNA methylation Libraries (IDOL)

Description Usage Arguments Value

View source: R/CandidateDMRFinder.v2.R

This function identifies candidate/putative differentially methylated loci (DML) based on the procedure described in Koestler et al., (2016). Breifly, a series of two-sample t-tests are fit to the J CpGs contained in the referenceBetas object and used to compare the mean methylation beta-values between each of the K cell type against the mean methylation beta-values computed across the remaining K - 1 cell types. Putative DMLs are identified by first rank ordering CpGs by their t-statistics, then taking the top M DMLs with the smallest and largest t-statistics for each of the K comparisons.

1 2	CandidateDMRFinder.v2(cellTypes, referenceBetas, referenceCovars, M = 150, equal.variance = F)

`cellTypes:`	A vector of length K that contains the cell type names. For example, c("CD4T", "CD8T", "NK", "Bcell", "Mono", "Gran").
`referenceBetas:`	A J x N matrix of cell-specific methylation beta-values; J represents the number of CpGs (i.e., ~ 450,000 for the Illumina HumanMethylation450 array) and N represents the number of samples for which cell-specific methylation signatures are available.
`referenceCovars:`	A N x P data.frame of meta data aross the N samples. The rows of this object MUST be in the same order as the columns of referenceBetas. Further, there must be a column called "CellType" (case sensitive), that indicates the cell-type identity for each of the N samples. The nomenclature used to indicate cell identity across the N samples should follow the nomenclature used for cellTypes (see above).
`M:`	The number of candidate DMLs with the smallest and largest t-statistic to return for each comparison. Defaults to M = 150 as in Koestler et al., (2016)
`equal.variance:`	Should a t-test assuming equal variances be fit. Defaults to FALSE, an unequal variance t-test.

A list containing two objects: (1) candidateSet - a vector containing the names of the R candidate DMLs identified from the analysis and (2) coefEsts - A R x K matrix of the within-cell type mean methylation beta values across the R identified candidate DMLs.

immunomethylomics/IDOL documentation built on July 9, 2020, 5:14 a.m.