I am trying to get gene symbols for gene ids that I got for mouse datasets. Gene ids look like that: 0610009B22Rik. The code that I am trying to utilize is the following one:
ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
mouse_gene_ids <- dataset[, 1]
foo <- getBM(attributes=c('ensembl_gene_id',
'external_gene_name'),
filters = 'genedb',
values = mouse_gene_ids,
mart = ensembl)
I am getting zero results as an output after the query runs. I guess filters parameter is wrong. Any suggestions would be greatly appreciated.
The filter you need is mgi_symbol e.g.
library(biomaRt)
ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
mouse_gene_ids <- "0610009B22Rik"
foo <- getBM(attributes=c('ensembl_gene_id',
'external_gene_name'),
filters = 'mgi_symbol',
values = mouse_gene_ids,
mart = ensembl)
Here's the result:
> foo
ensembl_gene_id external_gene_name
1 ENSMUSG00000007777 0610009B22Rik
I find the best way to choose the correct filter is to start with the Ensembl BioMart web interface, use the examples in the Filters -> external references ID list dropdown list to find the format I'm using, and then hit the XML button near the top. This will let you see the filter name required by biomaRt
library(biomaRt)
listMarts()
ensembl=useMart("ensembl")
datasets <- listDatasets(ensembl)
head(datasets)
ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)
entrzID=c("14455", "80904", "94275")
filters = listFilters(ensembl)
filters[1:50,]
getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "mgi_symbol", values = entrzID, mart = ensembl)
output:
[1] ensembl_gene_id external_gene_name
<0 rows> (or 0-length row.names)
Why can't I get any gene symbol
Perhaps you want to try the entrezgene_id filter instead?
getBM(attributes = c("ensembl_gene_id", "external_gene_name"),
filters = "entrezgene_id",
values = entrzID,
mart = ensembl)
ensembl_gene_id external_gene_name
1 ENSMUSG00000040415 Dtx3
2 ENSMUSG00000025151 Maged1
Hello, I tried to follow the previous posts and actually everything worked but I did not get anything back as result. My code below:
library(biomaRt)
ensembl <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
genes_ids <- c('ENSMUSG00000051951.5', 'ENSMUSG00000025900.12', 'ENSMUSG00000025902.13')
gs_heatdata <- getBM(attributes = c("external_gene_name"),
filters = "mgi_symbol",
values = genes_ids,
mart = ensembl)
Hi, you need to remove the trailing numbers from the gene IDs. Also, the value for filters should be ensembl_gene_id. Please try this:
library(biomaRt)
ensembl <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
genes_ids <- sub('\\.[0-9]*$', '',
c('ENSMUSG00000051951.5', 'ENSMUSG00000025900.12', 'ENSMUSG00000025902.13'))
gs_heatdata <- getBM(
attributes = c('external_gene_name', 'mgi_symbol','ensembl_gene_id'),
filters = 'ensembl_gene_id',
values = genes_ids,
mart = ensembl)
gs_heatdata
external_gene_name mgi_symbol ensembl_gene_id
1 Rp1 Rp1 ENSMUSG00000025900
2 Sox17 Sox17 ENSMUSG00000025902
3 Xkr4 Xkr4 ENSMUSG00000051951
it works perfectly but I did not understand how you managed it:
- the trailing number stands for the 0s before the actual id?
- could you explain me in particular what sub('\\.[0-9]*$', '', refers to?
thank you a lot!
sorry I forgot one more question. How can I make the code "cleaner"? because the output in the end shows me two features that are the same, the 'external_gene_name' and 'mgi_symbol'.
Thank you!
I tried with my all dataset but it did not work. I just have in return the empty table with the external_gene_name and ensembl_gene_id as headers.
library(biomaRt)
ensembl <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
genes_ids <- sub('\\.[0-9]*$', '', row.names(heatdata))
gs_heatdata <- getBM(attributes = c('external_gene_name', 'ensembl_gene_id'),
filters = "mgi_symbol",
values = genes_ids,
mart = ensembl)
head(heatdata)
T0medium T0medium T0medium T0LAL T0LAL T0LAL 6hLAL 6hLAL 6hLAL 6hIMQ
ENSMUSG00000051951.5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
ENSMUSG00000025900.12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
ENSMUSG00000025902.13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
ENSMUSG00000033845.13 8.635869 8.717134 8.644194 8.688051 8.729801 8.719839 8.522753 8.451425 8.588430 8.93282
ENSMUSG00000025903.14 9.244627 9.269090 9.357344 9.148911 9.297785 9.352155 9.265217 9.099127 9.255727 9.28542
ENSMUSG00000104217.1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000
6hIMQ 6hIMQ 16hLAL 16hLAL 16hLAL 16hIMQ 16hIMQ 16hIMQ
ENSMUSG00000051951.5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
ENSMUSG00000025900.12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
ENSMUSG00000025902.13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
ENSMUSG00000033845.13 8.838776 8.843039 8.541431 8.565437 8.534634 9.114412 9.122216 9.117485
ENSMUSG00000025903.14 9.392362 9.217806 9.207043 9.377954 9.266217 9.221498 9.238627 9.220453
ENSMUSG00000104217.1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Hi, the converted IDs are contained in gs_heatdata. You then have to align these to the rownames of heatdata, and then replace them with the external gene IDs (MGI symbols).
Hi, how can I align them? which function should I use? how can I then replace them with the external gene IDs? should I first convert the row.names of heatdata in the first column and then somehow combine the df gs_heatdata with the df heatdata?
thank you a lot! :)
Hi, please take a look at functions such as which() and match(), and other functions from dplyr (package) for matching data-frames.
A quick example:
array1 <- c('a','b','c','d','e','f','g')
array2 <- c('e','f','g','a','b','c','d')
idx <- match(array1, array2)
data.frame(array1 = array1, array2 = array2[idx])
array1 array2
1 a a
2 b b
3 c c
4 d d
5 e e
6 f f
7 g g
Hi, I tried for now with match() but I think it did not work.
matched_heatdata <- match(gs_heatdata, heatdata)
matched_heatdata
[1] NA NA
match() returns the indices [in heatdata] of the elements of gs_heatdata
What you likely need is:
idx <- match(
sub('\\.[0-9]*$', '', rownames(heatdata)),
gs_heatdata$ensembl_gene_id)
gs_heatdata <- gs_heatdata[idx,]
all(sub('\\.[0-9]*$', '', rownames(heatdata)) == gs_heatdata$ensembl_gene_id) # must return TRUE
ok, I try this. Just for me to understand: can I also just use the previous genes_ids or I have to put the entire sub('\\.[0-9]*$', '', rownames(heatdata)) in match() and after all()? thank you!!
It returned this:
idx <- match(sub('\\.[0-9]*$', '', rownames(heatdata)),gs_heatdata$ensembl_gene_id)
gs_heatdata <- gs_heatdata[idx,]
all(sub('\\.[0-9]*$', '', rownames(heatdata)) == gs_heatdata$ensembl_gene_id)
[1] NA
I think I found a problem and it was quite in front of me.
the filters set were wrong. I had to use filters = "ensembl_gene_id" instead of filters = "mgi_symbol".
now the gs_heatdata looks good:
external_gene_name ensembl_gene_id
3079 Xkr4 ENSMUSG00000051951
424 Rp1 ENSMUSG00000025900
425 Sox17 ENSMUSG00000025902
1951 Mrpl15 ENSMUSG00000033845
426 Lypla1 ENSMUSG00000025903
4321 Gm37988 ENSMUSG00000104217
but if I proceed with the previous code I get anyway NA:
idx <- match(sub('\\.[0-9]*$', '', rownames(heatdata)), gs_heatdata$ensembl_gene_id)
gs_heatdata <- gs_heatdata[idx,]
all(sub('\\.[0-9]*$', '', rownames(heatdata)) == gs_heatdata$ensembl_gene_id)
[1] NA
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I actually do not need any
gene ids, but thegene symbols, likedbl-1orilcr-1,il-17, etc. Whichattributesthen should I supply?Please use
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