batchQC_shapeVariation: Perform Mean and Variance batch variation analysis

In BatchQC: Batch Effects Quality Control Software

Description

Perform Mean and Variance batch variation analysis

Usage

batchQC_shapeVariation(
  data,
  groups,
  plot = FALSE,
  groupCol = NULL,
  robustSample = FALSE,
  robustGene = FALSE
)

Arguments

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

Value

Mean and Variance batch variation Overall and Pairwise p-values

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)
batchQC_shapeVariation(data.matrix, groups=batch)

BatchQC documentation built on Nov. 8, 2020, 8:30 p.m.