refFreeEWASP {RnBeads} | R Documentation

## 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

### 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.

[Package RnBeads version 2.10.0 Index]