tag: tag

In chr1swallace/GUESSFM: Using GUESS for Fine Mapping

Description

Derive tag SNPs for a SnpMatrix object using heirarchical clustering

Usage

tag(X, tag.threshold = 0.99, snps = NULL, samples = NULL, strata = NULL,
  quiet = FALSE, method = "single", split.at = 500)

Arguments

X	SnpMatrix object
tag.threshold	threshold to cut tree, default=0.99
snps	colnames of the SnpMatrix object to be used
samples	optional, subset of samples to use
strata	optional, return a list of tag vectors, one for each stratum defined by as.factor(strata)
quiet	if FALSE (default), show progress messages
method	method used for heirarchical clustering. See hclust for options.
split.at	for large numbers of SNPs, tag first splits them into subsets of size split.at with similar MAF, then groups tag groups in high LD between subsets. If you wish to avoid this, at additional computational cost, set split.at=NULL

Details

Uses complete linkage and the hclust function to define clusters, then cuts the tree at 1-tag.threshold

Value

character vector, names are snps, values are the tag for each SNP

Author(s)

Chris Wallace

chr1swallace/GUESSFM documentation built on May 13, 2019, 6:17 p.m.