Description Usage Arguments Value Examples
View source: R/shapeAnalysis.R
Perform Mean and Variance batch variation analysis
1 2 3 4 5 6 7 8 |
data |
Given data |
groups |
a character vector indicating sample group membership |
plot |
Indicate whether to generate plot |
groupCol |
group color |
robustSample |
Indicate whether to use robust sample-wise test |
robustGene |
Indicate whether to use robust gene-wise test |
Mean and Variance batch variation Overall and Pairwise p-values
1 2 3 4 5 6 7 8 | 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)
batchQC_shapeVariation(data.matrix, groups=batch)
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