BatchQC (version 1.0.17)

batchtest: 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)