GetResiduals: Get Residuals

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Description

Get Residuals

Usage

GetResiduals(
  dnam,
  betaToM = TRUE,
  pheno_df,
  covariates_char,
  nCores_int = 1L,
  ...
)

Arguments

dnam	data frame or matrix of methylation values, with row names = CpG IDs, column names = sample IDs. This is often the genome-wide array data. Note that if beta values are the input here, then betaToM should be set to TRUE. If mvalues are the input, then betaToM should be set to FALSE
betaToM	indicates if converting methylation beta values to mvalues
pheno_df	a data frame with phenotype and covariates, with variable Sample indicating sample IDs.
covariates_char	character vector for names of the covariate variables
nCores_int	Number of computing cores to be used when executing code in parallel. Defaults to 1 (serial computing).
...	Dots for additional arguments passed to the cluster constructor. See CreateParallelWorkers for more information.

Value

output a matrix of residual values, in the same dimension as dnam

Examples

   data(betasChr22_df)

   data(pheno_df)

   GetResiduals(
     dnam = betasChr22_df[1:10, 1:10],
     betaToM = TRUE,
     pheno_df = pheno_df,
     covariates_char = c("age.brain", "sex", "slide")
   )

lissettegomez/coMethDMR documentation built on April 25, 2021, 1:10 p.m.