batchtest {BatchQC} | R Documentation

## Performs test to check whether batch needs to be adjusted

### Description

Performs test to check whether batch needs to be adjusted

### Usage

    batchtest(pca, batch, mod = NULL)

### Arguments

`pca` | PCA object from principal component analysis
`batch` | Batch covariate
`mod` | Model matrix for outcome of interest and other covariates besides batch

### Value

Summary of linear regression of first five principal components

### 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)
    pca <- batchqc_pca(data.matrix, batch, mod=modmatrix)
    batchtest(pca, batch, mod=modmatrix)

[Package BatchQC version 1.6.1 Index]