| batchQC_filter_genes {BatchQC} | R Documentation |
Returns a datset after filtering genes of zero variance across batch and condition combinations
batchQC_filter_genes(data.matrix, batch, condition)
data.matrix |
Given data or simulated data from rnaseq_sim() |
batch |
Batch covariate |
condition |
Condition covariate of interest |
Filtered dataset after filtering genes of zero variance across batch and condition combinations
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)