| irwsva.build2 {ttScreening} | R Documentation |
Adjusted irwsva.build which builds surrogate variables from gene expression data
Description
This function is directly modified from the original irwsva.build() in the SVA package. It was noticed that under certain circumstances a subscript out of bounds error would occur while running the SVA function. Therefore, this modified code has a single line altered that conditionally uses the generic singular decomposition, svd(), instead of fast singular decomposition, fast.svd().
Usage
irwsva.build2(dat, mod, mod0 = NULL, n.sv, B = 5)
Arguments
dat |
A m CpG sites by n subjects matrix of methylation data. |
mod |
A n by k model matrix corresponding to the primary model fit (see model.matrix) |
mod0 |
A n by k0 model matrix corresponding to the null model to be compared to mod. |
n.sv |
The number of surrogate variables to construct. |
B |
The number of iterations of the algorithm to perform. |
Details
See http://www.bioconductor.org/packages/release/bioc/manuals/sva/man/sva.pdf
Value
sv |
A n by n.sv matrix where each column is a distinct surrogate variable. |
pprob.gam |
A vector with the posterior probability estimates that each row is affected by dependence. |
pprob.b |
A vector with the posterior probabiliity estimates that each row is affected by the variables in mod, but not in mod0. |
n.sv |
The number of suggorate variables estimated. |
Note
sva Vignette http://www.biostat.jhsph.edu/~jleek/sva/
Author(s)
Original irwsva.build: Jeffrey T. Leek <jleek@jhsph.edu>, John Storey jstorey@princeton.edu
References
Original sva: Leek JT and Storey JD. (2008) A general framework for multiple testing dependence.Proceedings of the National Academy of Sciences, 105: 18718-18723.
Leek JT and Storey JD. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics, 3: e161.