LD: max-statistic for a 2x3 table

In isglobal-brge/SNPassoc: SNPs-Based Whole Genome Association Studies

max-statistic for a 2x3 table

Description

Compute pairwise linkage disequilibrium between genetic markers

Usage

LD(g1, ...)

## S3 method for class 'snp'
LD(g1, g2, ...)

## S3 method for class 'setupSNP'
LD(g1, SNPs, ...)


LDplot(x, digits = 3, marker, distance, which = c("D", "D'",
    "r", "X^2", "P-value", "n", " "), ...)

LDtable(x, colorcut = c(0, 0.01, 0.025, 0.05, 0.1, 1), 
       colors = heat.colors(length(colorcut)),
       textcol = "black", digits = 3, show.all = FALSE, 
       which = c("D", "D'", "r", "X^2", "P-value", "n"), 
       colorize = "P-value", cex, ...)

Arguments

g1	genotype object or dataframe containing genotype objects
g2	genotype object (ignored if g1 is a dataframe)
SNPs	columns containing SNPs
x	LD or LD.data.frame object
digits	Number of significant digits to display
which	Name(s) of LD information items to be displayed
colorcut	P-value cutoffs points for colorizing LDtable
colors	Colors for each P-value cutoff given in 'colorcut' for LDtable
textcol	Color for text labels for LDtable
marker	Marker used as 'comparator' on LDplot. If omitted separate lines for each marker will be displayed
distance	Marker location, used for locating of markers on LDplot.
show.all	If TRUE, show all rows/columns of matrix. Otherwise omit completely blank rows/columns.
colorize	LD parameter used for determining table cell colors
cex	Scaling factor for table text. If absent, text will be scaled to fit within the table cells.
...	Optional arguments ('plot.LD.data.frame' passes these to 'LDtable' and 'LDplot').

Value

None

Author(s)

functions adapted from LD, LDtable and LDplot in package genetics by Gregory Warnes et al. ([e-mail])

References

genetics R package by Gregory Warnes et al. ([e-mail])

See Also

setupSNP snp

isglobal-brge/SNPassoc documentation built on May 15, 2023, 8:10 p.m.