BatchQC (version 1.0.17)

batchQC_fsva_adjusted: Use frozen surrogate variable analysis to remove the surrogate variables inferred from sva

Description

Use frozen surrogate variable analysis to remove the surrogate variables inferred from sva

Usage

batchQC_fsva_adjusted(data.matrix, modmatrix, sva.object)

Arguments

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

Value

Frozen Surrogate variables adjusted data

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)
sva.object <- batchQC_sva(data.matrix, mod=modmatrix)
batchQC_fsva_adjusted(data.matrix, modmatrix, sva.object)