Filter specific genes

The main use case for this function is the removal of sex-chromosome genes. Alternatively, filter genes that are not protein-coding.

Usage

filterGenes(
  obj,
  labels = c("X", "Y", "MT"),
  featureName = "chromosome_name",
  keepOnly = FALSE
)

Arguments

obj

ExpressionSet object.

labels

Labels of genes to filter or keep, eg. X, Y, and MT

featureName

FeatureData column name, eg. chr

keepOnly

Filter or keep only the genes with those labels

Value

Filtered ExpressionSet object

Examples

data(skin)
filterGenes(skin,labels = c('X','Y','MT'),featureName='chromosome_name')
filterGenes(skin,labels = 'protein_coding',featureName='gene_biotype',keepOnly=TRUE)