changeOrgDb {LINC} | R Documentation

## Change the Gene Annotation / Model Organism

### Description

The standard gene annotation in LINC is `"org.Hs.eg.db"`. This function is only relevant in case the input gene expression matrix is from another organism than Homo Sapiens.

### Usage

    changeOrgDb(object, OrgDb)

### Arguments

`object` | an instance of the `LINC` class
`OrgDb` | has to be one of: `c("org.Ag.eg.db", "org.At.tair.db", "org.Bt.eg.db", "org.Cf.eg.db", "org.Ce.eg.db", "org.Gg.eg.db", "org.Pt.eg.db", "org.Sco.eg.db", "org.EcK12.eg.db", "org.EcSakai.eg.db", "org.Dm.eg.db", "org.Tgondii.eg.db", "org.Hs.eg.db", "org.Pf.plasmo.db", "org.Mm.eg.db", "org.Ss.eg.db", "org.Rn.eg.db", "org.Mmu.eg.db", "org.Xl.eg.db", "org.Sc.sgd.db", "org.Dr.eg.db", "anopheles", "arabidopsis", "bovine", "canine", "celegans", "chicken", "chimp", "coelicolor", "ecolik12", "ecsakai", "fly", "gondii", "human", "malaria", "mouse", "pig", "rat", "rhesus", "xenopus", "yeast", "zebrafish")`

### Value

object with changed gene annotation hook

### Note

Please, also consider the documentation of clusterProfiler and ReactomePA.

### Author(s)

Manuel Goepferich

### Examples

    data(BRAIN_EXPR)

    # change the used gene annotation, here from "human" to "mouse"
    murine_matrix <- changeOrgDb(crbl_matrix, OrgDb = 'org.Mm.eg.db')

[Package LINC version 1.8.0 Index]