changeOrgDb: Change the Gene Annotation / Model Organism

In ManuelGoepferich/LINC: co-expression of lincRNAs and protein-coding genes

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')

ManuelGoepferich/LINC documentation built on May 7, 2019, 2:46 p.m.