Seurat (version 1.2.1)

batch.gene: Identify potential genes associated with batch effects

Description

Test for genes whose expression value is strongly predictive of batch (based on ROC classification). Important note: Assumes that the 'batch' of each cell is assigned to the cell's identity class (will be improved in a future release)

Usage

batch.gene(object, idents.use, genes.use = NULL, auc.cutoff = 0.6, thresh.use = 0)

Arguments

object

Seurat object

idents.use

Batch names to test

genes.use

Gene list to test

auc.cutoff

Minimum AUC needed to qualify as a 'batch gene'

thresh.use

Limit testing to genes which show, on average, at least X-fold difference (log-scale) in any one batch

Value

Returns a list of genes that are strongly correlated with batch.