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 rows are probes and columns are samples.

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. When the betas argument is a SummarizedExperiment object, this is ignored. colData(betas) will be used instead.

mc.cores

number of cores for parallel processing

Value

a list of test summaries, summary.lm objects

Examples

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

# release memory for Windows package builder
rm(list=ls(env=sesameData:::cacheEnv), envir=sesameData:::cacheEnv)
gc()


[Package sesame version 1.12.9 Index]