show.ld: show.ld

Description Usage Arguments Details Value Author(s)

Description

Calculate D' and R^2 for a SnpMatrix object and display as a heatmap

Usage

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2
  show.ld(X, snps = colnames(X), samples = rownames(X),
    lines.limit = 20)

Arguments

X

a SnpMatrix object

snps

optional character vector of column names of X (SNPs) for which LD should be calculated

samples

optional character vector of row names of X (Samples) for which LD should be calculated

lines.limit

draw faint lines to make separation between SNPs clearer if the number of SNPs is < lines.limit

Details

Side effect: displays plot on current graphics device

Value

invisibly returns matrix with D' in upper.tri() entries and R^2 in lower.tri() entries

Author(s)

Chris Wallace


chr1swallace/snpBMA documentation built on May 13, 2019, 6:19 p.m.