Hi,

I am getting difficulty in understanding what exactly p-value in listAttributes(FOR SNPs) indicate?

library(biomaRt)

mart<-useMart("ENSEMBL_MART_SNP", "hsapiens_snp", host = "www.ensembl.org")

listAttributes(mart)

25           phenotype_description                                        Phenotype description
26  associated_variant_risk_allele                               Associated variant risk allele
27                         p_value                                                      P value

Also, I am providing a list of RSID's  as values to getBM function but it tends to give me list of all snps from database instead of giving list of 5 snps.

vals<-c("rs10261247","rs10952923","rs12538777","rs1358064","rs1358065")
getsnp<- function(vals,mart){attr_4<- getBM(attributes =c("refsnp_id", "p_value", "minor_allele_freq", "minor_allele")
                                         ,values = vals , mart = mart)
           return(attr_4)}
SNPs<-getsnp(vals,mart)

This results in 351401 observations for 4 variables. It will be great if I can get any help on this. 

Thanks.

You are missing the filter argument, and if you don't provide that, you get everything (because you didn't say to filter on anything!).

Also do note that Ensembl doesn't have anything for those four SNPs anyway:

> vals<-c("rs10261247","rs10952923","rs12538777","rs1358064","rs1358065")

> getBM(c("refsnp_id", "p_value", "minor_allele_freq", "minor_allele"),"snp_filter",values = vals , mart = mart)
[1] refsnp_id         p_value           minor_allele_freq minor_allele     
<0 rows> (or 0-length row.names)

But if we add one more rsID, then we at least get some data.

> vals<-c("rs10261247","rs10952923","rs12538777","rs1358064","rs1358065", "rs61753175")
> getBM(c("refsnp_id", "p_value", "minor_allele_freq", "minor_allele"),"snp_filter",values = vals , mart = mart)
   refsnp_id p_value minor_allele_freq minor_allele
1 rs61753175      NA                NA           NA