Dear all,
I have a question regarding SNPs to genes mapping using BiomaRt.
I have successfully mapped my chr/start/end SNP positions to ENSIDs and gene symbols. I have done this several times but my question is; Can I keep my original SNP positions in the resulting file which has the chr-start-end gene positions and names? I struggle everytime I need to go back to the original SNP positions to link them to the genes I extracted from BiomaRt. As a picture is worth a 1000 words, please see below:
my file (examples of SNP positions):
chr start end
1 194972207 194972207
6 41187262 41187262
7 43120222 43120222
7 43120878 43120878
BiomaRt's gene results (examples of gene results):
chromosome_name start_position end_position ensembl_gene_id hgnc_symbol
1 119853316 119853748 ENSG00000227205 PFN1P9
1 119886304 119886927 ENSG00000226446 NOTCH2P1
1 119893533 119896515 ENSG00000134249 ADAM30
Therefore, I do have the gene list I requested based on my file's positions, but I do not have those positions in the resulting file. That would be really useful to have.
Any help would be greatly appreciated.
Thank you in advance
2 answers
What about using GenomicRanges to find the overlaps between the ranges of the two files? Like this: you have these 2 files, in which 2 SNPs belong to the ranges of PFN1P9 and NOTCH2P1 (in your example files there were no matches):
> SNP
chr start end
1 1 119853317 119853317
2 6 41187262 41187262
3 1 119893536 119893536
4 7 43120878 43120878
> biomart
chromosome_name start_position end_position ensembl_gene_id hgnc_symbol
1 1 119853316 119853748 ENSG00000227205 PFN1P9
2 1 119893533 119896515 ENSG00000134249 ADAM30
3 1 119886304 119886927 ENSG00000226446 NOTCH2P1
If they are data frame, convert them to GRanges:
library(GenomicRanges)
SNP.gr <- makeGRangesFromDataFrame(SNP, keep.extra.columns = T)
biomart.gr <- makeGRangesFromDataFrame(biomart,
start.field = "start_position",
end.field = "end_position",
keep.extra.columns = T)
Then, use the findOverlaps function to match coordinates between GRanges, like so:
hits <- findOverlaps(query = SNP.gr, subject = biomart.gr)
The hits objects gives you the matching positions between the 2 GRanges. With that info, you can do anything. Such as (a bit sloppy):
mcolsbiomart.gr)$chrSNP <- NA
mcolsbiomart.gr)$chrSNP[subjectHits(hits)] <- seqnamesSNP.gr)[queryHits(hits)]
mcolsbiomart.gr)$startSNP <- NA
mcolsbiomart.gr)$startSNP[subjectHits(hits)] <- startSNP.gr)[queryHits(hits)]
mcolsbiomart.gr)$endSNP <- NA
mcolsbiomart.gr)$endSNP[subjectHits(hits)] <- endSNP.gr)[queryHits(hits)]
And there's the object:
GRanges object with 3 ranges and 5 metadata columns:
seqnames ranges strand | ensembl_gene_id hgnc_symbol chrSNP startSNP endSNP
<Rle> <IRanges> <Rle> | <factor> <factor> <character> <integer> <integer>
[1] 1 119853316-119853748 * | ENSG00000227205 PFN1P9 1 119853317 119853317
[2] 1 119893533-119896515 * | ENSG00000134249 ADAM30 1 119893536 119893536
[3] 1 119886304-119886927 * | ENSG00000226446 NOTCH2P1 <NA> <NA> <NA>
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
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