Window size

[swvanderlaan]

Hi,

Just for clarification: is the window size read like ± xxxx kb around the index variant?

Thanks!

Sander

[slowkow]

The window is in bp, not kbp. The default is 1e5 or 100,000 bp.

That means 50,000 upstream and 50,000 downstream.

proxysnps/R/get_proxies.R

Lines 20 to 44 in 08637c7

	#' @param chrom a chromosome name (1-22,X) without "chr"
	#' @param pos a positive integer indicating the position of a SNP
	#' @param window_size a positive integer indicating the size of the window
	#' @param pop the name of a 1000 Genomes population (AMR,AFR,ASN,EUR,...). Set
	#' this to NA to use all populations.
	#' @return A dataframe with the following columns:
	#' \describe{
	#' \item{CHROM}{Chromosome name, e.g. "1"}
	#' \item{POS}{Position, e.g. 583090}
	#' \item{ID}{Identifier, e.g. "rs11063140"}
	#' \item{REF}{Reference allele, e.g. "A"}
	#' \item{ALT}{Alternative allele, e.g. "G"}
	#' \item{MAF}{Minor allele frequency, e.g. 0.1}
	#' \item{R.squared}{Squared Pearson correlation coefficient, e.g. 1.0}
	#' \item{D.prime}{D prime value, e.g. 1.0}
	#' \item{CHOSEN}{Binary indicator set to TRUE for the SNP of interest}
	#' }
	#'
	#' @examples
	#' d <- get_proxies(chrom = "12", pos = 583090, window_size = 1e5, pop = "AFR")
	#' head(d)
	#'
	#' @export
	get_proxies <- function(
	chrom = NA, pos = NA, query = NA, window_size = 1e5, pop = NA) {