sva.check: A function for post-hoc checking of an sva object to check...

In steveneschrich/msva: Surrogate Variable Analysis

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

Details

empirical.controls for a direct estimate of the empirical controls.

Value

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

Examples

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)

steveneschrich/msva documentation built on Dec. 23, 2021, 5:33 a.m.