batchQC_shapeVariation {BatchQC} | R Documentation |
Perform Mean and Variance batch variation analysis
batchQC_shapeVariation( data, groups, plot = FALSE, groupCol = NULL, robustSample = FALSE, robustGene = FALSE )
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
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)