Entering edit mode
Hi, all
I'm trying to get function information, nonsynonymous or synonymous, of all coding-area SNPs in chromosome 22 from biomaRt.
The code I tried is as below:
> require(biomaRt)
> mart <- useMart("snp")
> dataset <- useDataset("hsapiens_snp", mart=mart)
> filters <- listFilters(dataset)
> attributes <- listAttributes(dataset)
> snps.chr22 <- getBM(attributes=c('refsnp_id', 'chrom_start', 'minor_allele_freq', 'ensembl_gene_stable_id', 'consequence_type_tv'), filters='chr_name', values=22, mart=dataset)
> unique(snps.chr22$consequence_type_tv)
[1] "downstream_gene_variant" "upstream_gene_variant"
[3] "non_coding_exon_variant" "nc_transcript_variant"
[5] "3_prime_UTR_variant" "splice_region_variant"
[7] "synonymous_variant" "intron_variant"
[9] "NMD_transcript_variant" "missense_variant"
[11] "5_prime_UTR_variant" "stop_lost"
[13] "initiator_codon_variant" ""
[15] "feature_elongation" "feature_truncation"
[17] "stop_gained" "frameshift_variant"
[19] "splice_donor_variant" "inframe_insertion"
[21] "splice_acceptor_variant" "inframe_deletion"
[23] "coding_sequence_variant" "stop_retained_variant"
[25] "incomplete_terminal_codon_variant" "mature_miRNA_variant"
[27] "transcript_ablation"
There is nothing such as 'nonsynomynous' in consequence_type_tv. Even though there is a 'synonymous_variant' but that's not enough for me. Does anyone know if there is some other attribute(s) or filter(s) I can try to get such information? Thanks.
Best,
Ting
I think you already have that information; it has just been separated into the various types of non-synonymous variants that can occur. You just have to select the type(s) of non-synonymous variants you care about, and do whatever you want, based on those data.
Hi, James
Thank you for your response! So now I see that my code did bring me to the right place. And the next step is to recognize which of these variant types belong to nonsynonymous group. But I'm a statistician. Even though I'm taking biology class, it's still difficult for me to tell if some given variant type is a nonsynonymous one or not. Now I got 25 types of variants from 'consequence_type_tv'(excluding a " " and "synonymous_variant"). Could you please copy and paste the names of the nonsynonymous types here if that's not too much trouble?
Thank you very much!
http://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences
Scroll down to the table.
Thanks!!! That's really helpful!