mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

cis_trans

R Documentation

Annotate cis/trans SNPs

Description

Attempts to annotate SNPs as cis or trans depending on their location to the gene coding region. This is achieved using the 'biomaRt' R package.

Usage

cis_trans(
  dat,
  cis_region = 5e+05,
  chr_col = "chr.exposure",
  pos_col = "position.exposure",
  snp_col = NULL,
  values_col = "exposure",
  filter = "ensembl_gene_id",
  missing = "include",
  build = "grch37"
)

Arguments

`dat`	Data.frame of data
`cis_region`	Cis region definition (Optional, in kb)
`chr_col`	Column name for chromosome (Optional)
`pos_col`	Column name for position (Optional)
`snp_col`	Column name for SNP rsIDs (Optional)
`values_col`	Column name for gene names or ENSG IDs (Optional) NB: Choice must match the 'filter' value
`filter`	How to search for genes in biomaRt, either: "ensembl_gene_id" for ENSG IDs, or "hgnc_symbol" for gene names (Optional)
`missing`	"Include" or "drop" SNPs which could not be matched (Optional)
`build`	Genomic build (Optional)