R: max-statistic for a 2x3 table

LD {SNPassoc} | R Documentation

## 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. (warnes@bst.rochester.edu)

### References

genetics R package by Gregory Warnes et al. (warnes@bst.rochester.edu)

### See Also

`setupSNP` `snp`

[Package SNPassoc version 1.9-2 Index]