batchQC_filter_genes: Returns a datset after filtering genes of zero variance...

In BatchQC: Batch Effects Quality Control Software

Description

Returns a datset after filtering genes of zero variance across batch and condition combinations

Usage

batchQC_filter_genes(data.matrix, batch, condition)

Arguments

data.matrix	Given data or simulated data from rnaseq_sim()
batch	Batch covariate
condition	Condition covariate of interest

Value

Filtered dataset after filtering genes of zero variance across batch and condition combinations

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)
filtered.data <- batchQC_filter_genes(data.matrix, batch, condition)

Example output

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