batchtest {BatchQC} | R Documentation |
Performs test to check whether batch needs to be adjusted
batchtest(pca, batch, mod = NULL)
pca |
PCA object from principal component analysis |
batch |
Batch covariate |
mod |
Model matrix for outcome of interest and other covariates besides batch |
Summary of linear regression of first five principal components
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)