DML {sesame}R Documentation

Test differential methylation on each locus

Description

The function takes a beta value matrix with probes on the rows and samples on the columns. It also takes a sample information data frame (meta) and formula for testing. The function outputs a list of coefficient tables for each factor tested.

Usage

DML(betas, fm, meta = NULL, mc.cores = 1)

Arguments

betas

beta values, matrix or SummarizedExperiment

fm

formula

meta

data frame for sample information, column names are predictor variables (e.g., sex, age, treatment, tumor/normal etc) and are referenced in formula. Rows are samples.

mc.cores

number of cores for parallel processing

Value

a list of test summaries

Examples

sesameDataCache("HM450") # in case not done yet
data <- sesameDataGet('HM450.76.TCGA.matched')
smry <- summaryExtractSlope(DML(
    data$betas[1:1000,], ~type, meta=data$sampleInfo))

[Package sesame version 1.8.10 Index]