RnBeads (version 1.4.0)

refFreeEWASP: refFreeEWASP

Description

Applies the reference-free cell-type heterogeneity adjustment model from [1] and returns corrected p-values

Usage

refFreeEWASP(X, inds.g1, inds.g2 = -inds.g1, adjustment.table = NULL, paired = FALSE, nboot = 100, ignore.na = TRUE, rescale.residual = TRUE)

Arguments

X

Matrix on which the test is performed for every row

inds.g1

column indices of group 1 members

inds.g2

column indices of group 2 members

adjustment.table

a data.frame containing variables to adjust for in the testing

paired

should a paired analysis model be used. If so, the first index in inds.g1 must correspond to the first index in inds.g2 and so on.

nboot

The number of bootstrapping resamples

ignore.na

in this case all NA containing rows are removed

rescale.residual

rescale the residual matrix as z-scores

Value

vector of p-values for the "adjusted" regression coefficients from the Reference-free EWAS model

References

1. Houseman, E. Andres, John Molitor, and Carmen J. Marsit. "Reference-Free Cell Mixture Adjustments in Analysis of DNA Methylation Data." Bioinformatics (2014): btu029.