sva2: The adjusted sva code using irwsva.build2

Description

This function is the modified SVA function in which it uses the irwsva.build2 function rather than the irwsva.build function to build the surrogate variables. Thus, only a single line has been altered from the original SVA() function.

Usage

sva2(dat, mod, mod0 = NULL, n.sv = NULL, method = c("irw", "two-step"), 
	vfilter = NULL, B = 5, numSVmethod = "be")

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

Optional. The number of surrogate variables to estimate, can be estimated using the num.sv function.

method

Choose between the iteratively re-weighted or two-step surrogate variable estimation algorithms.

vfilter

The number of most variable CpG sites to use when building SVs, must be between 100 and m.

The number of iterations of the algorithm to perform.

numSVmethod

The method for determining the number of surrogate variables to use.

Value

svA n by n.sv matrix where each column is a distinct surrogate variable.
pprob.gamA vector with the posterior probability estimates that each row is affected by dependence.
pprob.bA vector with the posterior probabiliity estimates that each row is affected by the variables in mod, but not in mod0.
n.svThe number of suggorate variables estimated.

Details

See http://www.bioconductor.org/packages/release/bioc/manuals/sva/man/sva.pdf

References