drop: Remove from a GeneSetCollection

In llrs/GSEAdv: Analyze Gene Sets Collections Properites

Description

Removes either genes or pathways of a GeneSetCollection if present.

Usage

drop(object, gene, pathway)

## S4 method for signature 'GeneSetCollection,character,character'
drop(object, gene,
  pathway)

## S4 method for signature 'GeneSetCollection,missing,character'
drop(object, pathway)

## S4 method for signature 'GeneSetCollection,character,missing'
drop(object, gene)

## S4 method for signature 'GeneSetCollection,numeric,numeric'
drop(object, gene, pathway)

## S4 method for signature 'GeneSetCollection,missing,numeric'
drop(object, pathway)

## S4 method for signature 'GeneSetCollection,numeric,missing'
drop(object, gene, pathway)

Arguments

object	A GeneSetCollection object.
gene	The number or names of the genes to be removed.
pathway	The number or names of the pathways to be removed.

Value

A GeneSetCollection object without those genes or pathways.

Methods (by class)

• object = GeneSetCollection,gene = character,pathway = character: Drop genes and pathways

• object = GeneSetCollection,gene = missing,pathway = character: Drop pathways

• object = GeneSetCollection,gene = character,pathway = missing: Drop genes

• object = GeneSetCollection,gene = numeric,pathway = numeric: Drop the specified number of genes and pathways

• object = GeneSetCollection,gene = missing,pathway = numeric: Drop the specified number of pathway

• object = GeneSetCollection,gene = numeric,pathway = missing: Drop the specified number of genes.

Note

Remember that a GeneSet is defined as a group of genes (more than one), and if one gene set has only one gene it is removed. Conversely, a gene is removed if it doesn't belong to any GeneSet.

See Also

add To just add a relationship. modify To remove and add relationship at once.

Examples

drop(Info, gene = "3", pathway = "156580")
drop(Info, pathway = "156580")

llrs/GSEAdv documentation built on May 29, 2019, 6 p.m.