DML: Test differential methylation on each locus

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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, BPPARAM = SerialParam())

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. The row order of the data frame must match the column order of the beta value matrix.
BPPARAM	number of cores for parallel processing, default to SerialParam() Use MulticoreParam(mc.cores) for parallel processing. For Windows, try DoparParam or SnowParam.

Value

a list of test summaries, summary.lm objects

Examples

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

sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.