Annotate merged fine-mapping results from all loci

Annotate fine-mapping results from echolocatoR across all loci.

annotate_snps(
  dat,
  SNP_col = "SNP",
  haploreg_annotation = TRUE,
  regulomeDB_annotation = TRUE,
  biomart_annotation = TRUE,
  verbose = TRUE
)

Arguments

dat

Table containing at least a SNP column.

SNP_col

Name of the column in dat that contain's each SNPs RSID.

haploreg_annotation

Annotate SNPs with HaploReg (using HaploR).

regulomeDB_annotation

Annotate SNPs with regulomeDB (using HaploR).

biomart_annotation

Annotate SNPs with biomart.

verbose

Print messages.

Examples

dat <- echodata::BST1[Consensus_SNP==TRUE,]
dat_annot <- annotate_snps(dat = dat)
#> Loading required namespace: haploR
#> + Gathering annotation data from HaploReg...
#> ++ Submitting chunk 1 / 1
#> + Gathering annotation data from HaploReg...
#> ++ Submitting chunk 1 / 1
#> No encoding supplied: defaulting to UTF-8.
#> No encoding supplied: defaulting to UTF-8.
#> No encoding supplied: defaulting to UTF-8.
#> No encoding supplied: defaulting to UTF-8.
#> + Gathering annotation data from Biomart...