getBackground: Get the background of molecules

In SubpathwayGMir: Identify Metabolic Subpathways Mediated by MicroRNAs

Description

getBackground attempts to get the background of user-specified molecules.

Usage

getBackground(type = "gene_miRNA")

Arguments

type	A character string. Should be one of "gene", "miRNA" or "gene_miRNA".

Details

The default background is obtained from the environment variable. For human, the reference gene background is all human genes in KEGG pathways. The reference miRNA background is collected from miRBase database.

Value

A character vector.

Author(s)

Li Feng, Chunquan Li and Xia Li

See Also

identifyGraph

Examples

## Not run: 
## get all background of genes
 bgGene <- getBackground(type="gene")

## get all background of miRNAs
 bgMir  <- getBackground(type="miRNA")

## get all background of miRNAs and genes
 bgGMir <- getBackground(type="gene_miRNA")

## End(Not run)

SubpathwayGMir documentation built on May 2, 2019, 2:39 a.m.