as.background {background} R Documentation

cast the cluster data as the enrichment background

Description

Usage

as.background(clusters,
    background.size = -1,
    name = "n/a",
    tax.id = "n/a",
    desc = "n/a",
    is.multipleOmics = FALSE,
    filter.compoundId = TRUE,
    kegg.code = NULL);

Arguments

clusters

a data cluster or a collection of kegg pathway model

background.size

default value -1 or zero means auto evaluated. [as integer]

name

the background model name. [as string]

tax.id

ncbi taxonomy id of the target organism. [as string]

desc

the model description. [as string]

is.multipleOmics

Create a enrichment background model for run multiple omics data analysis? this parameter is only works for the kegg pathway model where you are speicifc via the `clusters` parameter. [as boolean]

filter.compoundId

do compound id filtering when target model is `is_multipleOmics`? (all of the KEGG drug id and KEGG glycan id will be removed from the cluster model). [as boolean]

kegg.code

the kegg organism code when the given `clusters` collection is a collection of the pathway object. [as string]

env

[as Environment]

Details

Authors

gseakit

Value

this function returns data object of type Background.

clr value class

Examples


[Package background version 1.0.0.0 Index]