find_nearest_gene: Annotates nearest gene for list of SNPs

In oyhel/vautils: Various Utilities That I Never Find When I Need

Description

Finds the nearest gene for a list of markers. The input data expects a data frame with headers: rsid, chromosome, position. The list of annotations are obtained from PLINK documentation https://www.cog-genomics.org/plink/1.9/resources/

Usage

find_nearest_gene(data, flanking = 100, build = "hg19",
  collapse = TRUE, snp = "rsid", chr = "chromosome",
  bp = "position")

Arguments

data	dataframe with results
flanking	flanking distance (in kB) on each side (ie. 20kb = spans 40kb) defaults to 100kb (spans 200kb)
build	string specifying build (hg19 (default), hg18, hg38)
collapse	if TRUE (default) collapses nearest genes into single commasep. line. If FALSE returns all annotated genes on separate lines with a 'distance' column showing how many bp upstream (+) or downstream(-) the SNP is located
snp	snp column name in input data
chr	chromosome column name in input data
bp	position/bp column name in input data

Value

data frame with nearest gene specified per marker

oyhel/vautils documentation built on Nov. 14, 2019, 4:38 p.m.