tag: tag

Description Usage Arguments Details Value Author(s)

Description

Derive tag SNPs for a SnpMatrix object using heirarchical clustering

Usage

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2
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.