genes in rhesus genome (ref. TxDb.Mmulatta.UCSC.rheMac8.refGene)
1
0
Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 3.5 years ago
United States

Hi,

I was trying to do some comparative analysis between the rhesus and human genes. I seem to get no genes that are common to both species! What am I doing wrong? My code, screen output :

 

=============

library("TxDb.Hsapiens.UCSC.hg38.knownGene")
library("org.Hs.eg.db")

library("TxDb.Mmulatta.UCSC.rheMac8.refGene")
library("org.Mmu.eg.db")


txdb_hg38 <- TxDb.Hsapiens.UCSC.hg38.knownGene
txdb_rh8 <- TxDb.Mmulatta.UCSC.rheMac8.refGene

## All rhesus entrez ids

grgenes <- genes(txdb_rh8)
allrefs <- grgenes$gene_id 
monkey_entrez <- sort(mapIds(org.Mmu.eg.db, keys=allrefs, column="ENTREZID", keytype="REFSEQ", multiVals="filter"))


# homo sapiens entrez ids
grgenes <- genes(txdb_hg38)
human_entrez <- unique(grgenes$gene_id)

> length(monkey_entrez)
[1] 6371
> length(human_entrez)
[1] 24183
> length(intersect(monkey_entrez,human_entrez))
[1] 0
> head(monkey_entrez)
NM_001098400 NM_001105170 NM_001104552 NM_001105171 NM_001105172 NM_001105173 
 "100049578"  "100125558"  "100125559"  "100125560"  "100125562"  "100125563" 
> head(human_entrez)
[1] "1"         "10"        "100"       "1000"      "100009613" "100009676"

 

===========

 

Also, how can I get mapIds to return all matches (and not just 1:1)? I tried all the options for multiVals, but they all return the same number of entrez genes.

org.hs.eg.db org.mmu.eg.db • 902 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States

You seem to think that Gene IDs are species agnostic. They are not. A given Gene ID is for a gene found in a particular species.

If you want to map between species, you can use the biomaRt package, particularly the getLDS function.
 

ADD COMMENT

Login before adding your answer.

Traffic: 687 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6