Code snippets for R-package biomaRt.

biomart-snippets.Rmd

Here are some extra (unpolished) code snippets for the R-package `biomaRt` that came up during the writing of the [blogpost](https://sinarueeger.github.io/content/post/2018-07-27-GWAS-annotation). 

## Extract all SNPs for a particular genomic region

```{r, get-snp-info-pos-chr, include = TRUE, cache=TRUE, eval=FALSE}

library(biomaRt)

## select mart
snpmart = useMart(biomart = "ENSEMBL_MART_SNP", dataset="hsapiens_snp")

## extract SNPs
getBM(attributes = c('refsnp_id','allele','chrom_start','chrom_strand'), 
      filters = c('chr_name','start','end'), 
      values = list(8,148350,148612), 
      mart = snpmart)

```

## Get info about one gene, and extract all SNPs

```{r, get-gene-info, include = TRUE,cache =TRUE, eval=FALSE}

## first, we need to figure out the gene ID of FTO

## select mart
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")

## list all the filters 
listFilters(ensembl)

## list all attributes
listAttributes(ensembl)

## run
gene.name.fto <- getBM(attributes = c('ensembl_gene_id'), 
      filters = c('external_gene_name'),
      values = "FTO", 
      mart = ensembl)
gene.name.fto

## Now we want to get the range of SNPs for that gene
snps.fto <- getBM(attributes = c( 'refsnp_id',
  'chr_name',
  'chrom_start',
  'chrom_end'), 
      filters = c('ensembl_gene'),
      values = gene.name.fto$ensembl_gene_id, 
      mart = variation)

```