posibatches: Adjust for positional effects and batch effects using...

In ChuanJ/JCPackage: Adjust for positional and batch effects using ComBat

Description

posibatch allows users to adjust for positional effects and batch effects in Illumina Beadchips. Positional effects means the same sample in different physical positions on the array could be measured as different methylation or expression levels, and batch effects. Batch effects are sub-groups of measurements that have qualitatively different behaviour across conditions and are unrelated to the biological or scientific variables in a study. It uses either parametric or non-parametric empirical Bayes frameworks for adjusting data for positional effects and batch effects. Users are returned an expression or methylation matrix that has been corrected for position effects and batch effects. The input data are assumed to be cleaned and normalized before batch effect removal.

Usage

posibatches(dat, Sentrix, posi = TRUE, batch = TRUE, par.prior = TRUE,
  prior.plots = FALSE, mean.only.posi = FALSE, mean.only.batch = FALSE)

Arguments

dat	Genomic measure matrix (dimensions probe x sample) - for example, expression matrix
Sentrix	The list of position numbers and chip numbers - for example, sampleID, sampleNames (8963303124_R01C01) and batches
posi	Position covariate
batch	Batch covariate
par.prior	(Optional) TRUE indicates parametric adjustments will be used, FALSE indicates non-parametric adjustments will be used
prior.plots	(Optional) TRUE give prior plots with black as a kernel estimate of the empirical batch effect density and red as the parametric
mean.only.posi	(Optional) FALSE If TRUE posibatch only corrects the mean of the positional effect (no scale adjustment). If one position has only one sample, setting mean.only=TRUE.
mean.only.batch	(Optional) FALSE If TRUE posibatch only corrects the mean of the batch effect (no scale adjustment). If one batch has only one sample, setting mean.only=TRUE.
mod	Model matrix for outcome of interest and other covariates besides batch and position

Value

data A probe x sample genomic measure matrix, adjusted for positional effects and batch effects.

ChuanJ/JCPackage documentation built on May 23, 2019, 8:25 p.m.