| batchQC_svregress_adjusted {BatchQC} | R Documentation |
Regress the surrogate variables out of the expression data
batchQC_svregress_adjusted(data.matrix, modmatrix, sva.object)
data.matrix |
Given data or simulated data from rnaseq_sim() |
modmatrix |
Model matrix for outcome of interest and other covariates besides batch |
sva.object |
SVA object |
Surrogate variables regress adjusted 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)
sva.object <- batchQC_sva(data.matrix, mod=modmatrix)
batchQC_svregress_adjusted(data.matrix, modmatrix, sva.object)