| batchQC_sva {BatchQC} | R Documentation |
Estimate the surrogate variables using the 2 step approach proposed by Leek and Storey 2007
batchQC_sva(data.matrix, modmatrix)
data.matrix |
Given data or simulated data from rnaseq_sim() |
modmatrix |
Model matrix for outcome of interest and other covariates besides batch |
Surrogate variables analysis object
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)