filterGenes: Filter specific genes

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

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)

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.