getBackgroundLnc: Get the background of molecules

In SubpathwayLNCE: Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

Description

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

Usage

getBackgroundLnc(type = "gene_lncRNA")

Arguments

type	A character string. Should be one of "gene", "lncRNA" or "gene_lncRNA".

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 lncRNA background is collected from GeneCode database.

Value

A character vector.

Author(s)

Xinrui Shi, Chunquan Li and Xia Li

See Also

identifyLncGraphW

Examples

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

## get all background of lncRNAs
 bgLncRNA  <- getBackgroundLnc(type="lncRNA")

## get all background of lncRNAs and genes
 bgGL <- getBackgroundLnc(type="gene_lncRNA")

## End(Not run)

SubpathwayLNCE documentation built on May 1, 2019, 10:25 p.m.