Minor alleles giving NA from R biomart getBM?

Does anyone know how to extract minor allele data from grch38 ? the following gives NAs: library("biomaRt"); snp.db3 <- useMart(host = "https://www.ensembl.org/", biomart = "ENSEMBL_MART_SNP", dataset = "hsapiens_snp"); nt.biomart3 <- getBM(attributes = c("refsnp_id", "minor_allele", "minor_allele_freq", "chrom_start", "chrom_strand", "associated_gene"), filters = c("snp_filter"), values = c("rs3762444", "rs284262", "rs655598", "rs12089815", "rs12140153", "rs788163", "rs1064213", "rs1106090", "rs7557796", "rs16825008"), mart = snp.db3, uniqueRows = TRUE); nt.biomart3 The data is apparently available on Ensembl (e.g. https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=10:120308754-120309754;v=rs10788066;vdb=variation;vf=654619804) but the data extraction method only works if I use host = "https://grch37.ensembl.org" - otherwise it gives NAs for minor allele and minor allele frequency - is there something else I should do ? Or is there a better method ? Or is the minor allele data from grch37 actually up-to-date ?

Solution

Online Biomart (Martview) from Ensembl (https://www.ensembl.org/) doesn't show either this information :

That explains why you're getting "NA" with "biomaRt".

Online Biomart (Martview) from Ensembl GRCh37 (https://grch37.ensembl.org/) displays it :

Grch37 seems up to date (Release 112 (May 2024)).

To produce the preceding screenshots :

Go to https://www.ensembl.org/biomart/martview or https://grch37.ensembl.org/biomart/martview
Choose database -> "Ensembl Variation 112"
Choose dataset -> "Human Short Variants (SNPs and indels excluding flagged variants) (GRCh38.p14)"
Filters -> "General Variant Filters" -> Tick "Filter by Variant name" and specify the SNPs in the textbox
Attributes -> Variant -> "Variant Associated Information" -> Tick "Minor allele (ALL)" & "Global minor allele frequency (all individuals)"
Push on the buton "Results" at the top of the page

If you want data from Grch38, you can try to scrape the data directly from "Ensembl.org".

### Packages
library(rvest)
library(purrr)
library(dplyr)

### SNPs to look for
look=c("rs3762444", "rs284262", "rs655598", "rs12089815", "rs12140153", "rs788163", "rs1064213", "rs1106090", "rs7557796", "rs16825008")

### Function to get the data
biomart=function(x){
  z=read_html(paste0("http://www.ensembl.org/homo_sapiens/Variation/Explore?v=",x))
  a= z %>% 
    html_element(xpath = '//span[.="Highest population MAF"]/following-sibling::span/b') %>%
    html_text2()
  if (is.na(a)) {b<-NA_character_}else{
    b = z %>% 
    html_element(xpath = '//span[.="Highest population MAF"]/following-sibling::span') %>%
    html_attr("title") %>%
    read_html() %>% html_text2()}
  data.frame(SNP=x,MAF=a,source=b)
  }

### Map operation
out=map(look,biomart,.progress = TRUE)

### Build the dataframe
output=bind_rows(out)

Output :

         SNP  MAF                       source
1   rs3762444 <NA>                         <NA>
2    rs284262 0.49 T in 1000GENOMES:phase_3:SAS
3    rs655598 0.49 A in 1000GENOMES:phase_3:FIN
4  rs12089815 0.50 G in 1000GENOMES:phase_3:EUR
5  rs12140153 0.18             T in gnomADg:ami
6    rs788163 0.42 C in 1000GENOMES:phase_3:LWK
7   rs1064213 0.50             A in gnomADe:nfe
8   rs1106090 0.50             A in gnomADg:amr
9   rs7557796 0.48 T in 1000GENOMES:phase_3:SAS
10 rs16825008 0.49 A in 1000GENOMES:phase_3:ITU

Notes :

operation takes approximately a minute to complete for these 10 SNPs (ensembl.org servers seems overloaded) ;
rs3762444 is "NA" since there're 2 locations for this SNP. Some more lines of code would be needed to fix this issue.