The conversion Ensembl ID into Gene symbol
1
0
Entering edit mode
5 months ago
rufusek500 • 0

Hello, I want to convert my ensembl ID into gene symbol using biomart, but it occurred an error so called "could not find function "biomaRt". Could you advise me what am supposed to do? Below there is my command:

h1 = biomaRrt( genes=mygenelist_up6hours,mart="ENSEMBL_MART_ENSEMBL", dataset =
"hsapiens_gene_ensembl",filter = "ensembl_gene_id", attributes
="hgnc_symbol")

biomart • 503 views
1
Entering edit mode

Hi, you have a typo in your command, "biomaRrt".

0
Entering edit mode

What do you mean a typo in my command?

1
Entering edit mode

A double r in "biomaRrt".

But nevermind, the function you are looking for to map ensembl IDs to gene symbols is getBM. For example, as done here.

Also see this previous question: ENSEMBL Gene ID to Gene Symbol

0
Entering edit mode

Why not following what the error is telling you? Maybe to import the library before usage (if it's installed into your machine)?

0
Entering edit mode

I have imported the library before usage, but it seems to me that the problem pertains to the function than package.

0
Entering edit mode
5 months ago
Mike Smith ★ 2.0k

There is a difference between the command you have posted and the error message you show namely biomaRrt vs biomaRt. Note there is an extra r in the first.

However, I think the really problem is that the package {biomaRt} doesn't have a function biomaRt(). It looks to me like you first want to load the library and select the Ensembl Human Genes dataset via:

library(biomaRt)
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")


and then you can query it using the function getBM(), which would be something like this:

getBM(attributes = 'hgnc_symbol',
filters = 'ensembl_gene_id',
values = my_gene_list,
mart = ensembl)


You can read the full documentation at https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html

Alternatively, perhaps you're trying to use the {biomartr} package, which provides some wrappers around the {biomaRt} but uses different function names. I think that has a biomart() function (note that it's all lower case - that's important in R!).

0
Entering edit mode

Yes, you were right! Thanks a lot for your help