gene ID RNAseq
Hi friends How can I get gene numeric ID and hugo ID by R script? what script should I use? I have this but does not give numeric ID and hugo ID.
ibrary(biomaRt)
library(dplyr)
library(tibble)
attributeNames <-c("ensembl_gene_id","external_gene_name","HGNC_ID", "chromosome_name","description")
filterValues <- rownames(res)
Annotations <- getBM(attributes=attributeNames, filters =
"ensembl_gene_id",values = filterValues,
mart=useMart(biomart="ensembl",
dataset="hsapiens_gene_ensembl"))
• 2,087 views
•
link
updated
by
abedkurdi10 •
•
written
by
Rob •
•
written
by
Rob •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Issue with converting Affy IDs to gene IDs/symbols
written by rbronste
-
biomaRt crashes R studio
written by gernophil •
-
UniProt ID, genes
written by Rob •
-
Missing genes in converting "ensembl_gene_id_version" to "ensembl_gene_id" in biomaRt package
written by Maryam •
-
converting ensembl transcript ID to symbol
written by Maka •
-
gene ensemble ID- no symbol
written by Rob •
-
annotation - biomaRt - Error in UseMethod
written by ferreira.cristina •
-
What is the gold standard for the one-to-many relationships in BioMart retrieved annotations and ad…
written by 2405592M
-
annotation - biomaRt - getBM - multiple entrez ID
written by Learner
-
Map ensembl gene id form hg38 in hg19
written by Tanvir Ahamed
What do you mean by numeric ID?
Hi genes have IDs like 11243, and whatever number that is gene ID. I dont know how and where to get thm.
Do you mean entrez ID?
yes, I assume it is called entrez ID
use this:
attributeNames <-c("ensembl_gene_id","external_gene_name","hgnc_id", "chromosome_name","description","entrezgene_id")