Last data update: 2014.03.03
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R: A function for estimating the probability that each gene is...
empirical.controls | R Documentation |
A function for estimating the probability that each gene is an empirical control
Description
This function uses the iteratively reweighted surrogate variable analysis approach
to estimate the probability that each gene is an empirical control.
Usage
empirical.controls(dat, mod, mod0 = NULL, n.sv, B = 5, type = c("norm",
"counts"))
Arguments
dat |
The transformed data matrix with the variables in rows and samples in columns
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mod |
The model matrix being used to fit the data
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mod0 |
The null model being compared when fitting the data
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n.sv |
The number of surogate variables to estimate
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B |
The number of iterations of the irwsva algorithm to perform
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type |
If type is norm then standard irwsva is applied, if type is counts, then the moderated log transform is applied first
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Value
pcontrol A vector of probabilites that each gene is a control.
Results
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