sva.check: A function for post-hoc checking of an sva object to check for
degenerate cases.
Description
This function is designed to check for degenerate cases in the
sva fit and fix the sva object where possible.
Usage
sva.check(svaobj, dat, mod, mod0)
Arguments
svaobj
The transformed data matrix with the variables in rows and samples in columns
dat
The data set that was used to build the surrogate variables
mod
The model matrix being used to fit the data
mod0
The null model matrix being used to fit the data
Value
sv The estimated surrogate variables, one in each columnpprob.gam: A vector of the posterior probabilities each gene is affected by heterogeneitypprob.b A vector of the posterior probabilities each gene is affected by modn.sv The number of significant surrogate variables