DML {sesame} | R Documentation |
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.
DML(betas, fm, meta = NULL, mc.cores = 1)
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 |
a list of test summaries, summary.lm objects
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()