filterGenes: Filter specific genes

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Filter specific genes

Description

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)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.