BioMart : Retrieve set_gene_id (ENSG) and set_transcript_id (ENST) from SNPs rsIDs
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0
Entering edit mode
5.0 years ago

Hello, I want to retrieve set_gene_id (ENSG), set_transcript_id (ENST) from a file containing the rsIDs of many SNPs. After a lot of research, the BioMart package from R would allow me to do this. After some research, I saw that I had to use the argument refsnp_id to tell the program that I wanted to provide them with the rsIDs of my SNPs to perform the search and retrieve the gene and transcript ID.

Here is the code:

library(biomaRt)
Data <- readLines ("rsID.txt")
length(Data)

for (i in 1:length(Data)){
  mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
  results <- getBM(attributes = c("refsnp_id", "ensembl_gene_id", "ensembl_transcript_id"),
                   filters = "refsnp_id", values = "i",
                   mart = mart)
}

However, it returns the following error :

Error in getBM(attributes = c("refsnp_id", "ensembl_gene_id", "ensembl_transcript_id"),  : 
  Invalid attribute(s): refsnp_id 
Please use the function 'listAttributes' to get valid attribute names

How to tell it that I want to give him rsIDs ?

Second, is this the right way to read a txt file line by line and thus search for gene and transcript names for each sNP?

Thank you in advance for your help.

snp BioMart rs ID • 2.5k views
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2
Entering edit mode
5.0 years ago

You need to use a different mart. Take a look at my answer, here: A: How to retrieve Gene name from SNP ID using biomaRt

To see all attributes that are available, type:

listAttributes(mart)

Kevin

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2
Entering edit mode
5.0 years ago
Mike Smith ★ 2.0k

As Kevin says, you need to use the SNPs mart rather than the Genes mart.

You also don't need to do this inside a loop. You can provide a vector of rsIDs to the values argument and the function will run the query for all of them. This will be much faster than doing them one at a time within the loop.

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0
Entering edit mode
5.0 years ago

Thank you for your answers, indeed, I should not use biomart correctly and especially not be in snp mode. But how do I transform my text file into a vector? I've tried different commands that always send me the same message. How to do this?

What has been tried:

Data_vec <- as.vector(Data) 
Data_vec<-c("Data")

library(biomaRt) Data <- readLines ("file.txt") length(Data)

#Data_vec <- as.vector(Data) 
#Data_vec<-c(Data)

 require(biomaRt) ensembl <- useMart("ENSEMBL_MART_SNP", dataset =
"hsapiens_snp") getBM(attributes=c(   "refsnp_id",
"ensembl_gene_stable_id", "ensembl_transcript_stable_id"),  
filters="snp_filter", values="Data_vec",   mart=ensembl, uniqueRows=TRUE)

Error :

[1] refsnp_id                    ensembl_gene_stable_id       ensembl_transcript_stable_id
<0 rows> (or 0-length row.names)
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