refFreeEWASP: refFreeEWASP

In RnBeads: RnBeads

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

Note

Requires the package RefFreeEWAS.

Author(s)

Pavlo Lutsik

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.

RnBeads documentation built on March 3, 2021, 2 a.m.