batchQC_analyze {BatchQC} | R Documentation |
Checks for presence of batch effect and reports whether the batch needs to be adjusted
batchQC_analyze(data.matrix, batch, mod = NULL)
data.matrix |
Given data or simulated data from rnaseq_sim() |
batch |
Batch covariate |
mod |
Model matrix for outcome of interest and other covariates besides batch |
pca Principal Components Analysis object of the data
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_analyze(data.matrix, batch, mod=modmatrix)