refFreeEWASP {RnBeads} | R Documentation |
Applies the reference-free cell-type heterogeneity adjustment model from [1] and returns corrected p-values
refFreeEWASP( X, inds.g1, inds.g2 = -inds.g1, adjustment.table = NULL, paired = FALSE, nboot = 100, ignore.na = TRUE, rescale.residual = TRUE )
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 |
paired |
should a paired analysis model be used. If so, the first index in |
nboot |
The number of bootstrapping resamples |
ignore.na |
in this case all |
rescale.residual |
rescale the residual matrix as z-scores |
vector of p-values for the "adjusted" regression coefficients from the Reference-free EWAS model
Requires the package RefFreeEWAS.
Pavlo Lutsik
1. Houseman, E. Andres, John Molitor, and Carmen J. Marsit. "Reference-Free Cell Mixture Adjustments in Analysis of DNA Methylation Data." Bioinformatics (2014): btu029.