batchQC_sva {BatchQC} | R Documentation

## Estimate the surrogate variables using the 2 step approach proposed by Leek and Storey 2007

### Description

Estimate the surrogate variables using the 2 step approach proposed by Leek and Storey 2007

### Usage

    batchQC_sva(data.matrix, modmatrix)

### Arguments

`data.matrix` | Given data or simulated data from rnaseq_sim()
`modmatrix` | Model matrix for outcome of interest and other covariates besides batch

### Value

Surrogate variables analysis object

### Examples

    nbatch <- 3
    ncond <- 2
    npercond <- 10
    data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
        npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800,
        basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
    batch <- rep(1:nbatch, each=ncond*npercond)
    condition <- rep(rep(1:ncond, each=npercond), nbatch)
    pdata <- data.frame(batch, condition)
    modmatrix = model.matrix(~as.factor(condition), data=pdata)
    batchQC_sva(data.matrix, modmatrix)

[Package BatchQC version 1.6.1 Index]