batchQC_analyze: Checks for presence of batch effect and reports whether the...

Description Usage Arguments Value Examples

Description

Checks for presence of batch effect and reports whether the batch needs to be adjusted

Usage

1

Arguments

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

Value

pca Principal Components Analysis object of the data

Examples

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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)


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