A function for post-hoc checking of an sva object to check for degenerate cases.
This function is designed to check for degenerate cases in the sva fit and fix the sva object where possible.
sva.check(svaobj, dat, mod, mod0)
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 |
empirical.controls for a direct estimate of the empirical controls.
sv The estimated surrogate variables, one in each column
pprob.gam: A vector of the posterior probabilities each gene is affected by heterogeneity
pprob.b A vector of the posterior probabilities each gene is affected by mod
n.sv The number of significant surrogate variables
library(bladderbatch) data(bladderdata) #dat <- bladderEset dat <- bladderEset[1:5000,] pheno = pData(dat) edata = exprs(dat) mod = model.matrix(~as.factor(cancer), data=pheno) mod0 = model.matrix(~1,data=pheno) n.sv = num.sv(edata,mod,method="leek") svobj = sva(edata,mod,mod0,n.sv=n.sv) svacheckobj = sva.check(svobj,edata,mod,mod0)
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