genotypeSummary {GeneticsBase} | R Documentation

## print the summary of genotypes sorted by markers

### Description

print the summary of genotypes sorted by markers

### Usage

    genotypeSummary(object,
                    by = NULL,
                    confidence = 0.95,
                    alpha = 1 - confidence,
                    show = TRUE,
                    HWE.method = c("simulate", "exact"),
                    simulate.p.value = TRUE,
                    B = 10000,
                    verbose = FALSE,
                    includeOverall = FALSE,
                    omitRepeats = TRUE,
                    founderOnly = TRUE,
                    ...)

### Arguments

`object` | geneSet object
`by` | optional column name, by which the summary is desired. Default is NULL.
`confidence` | confidence intervals of Genotype frequencies within each marker (default is 95%)
`alpha` | Type -1 error rate = (1- confidence)
`show` | No longer used
`HWE.method` | Method to be used for Hardy-Weinberg Equilibrium Significance Test, exact or simulate
`simulate.p.value` | No longer used
`B` | No longer used
`verbose` | No longer used
`includeOverall` | logical value (TRUE/FALSE) indicating whether overall summary is also needed, default = FALSE
`omitRepeats` | logical value (TRUE/FALSE) indicating whether Gene name and marker name should be printed repeatedly for each Genotype, default = TRUE
`founderOnly` | logical value (TRUE/FALSE) indicating whether founder information should be extracted from the geneSet object, default = TRUE
`...` | any further arguments to print

### Details

We can print the genotypeSummary on screen, or save in .html format or .tex format

### Author(s)

Nitin Jain nitin.jain@pfizer.com

### Examples

    library(GeneticsBase)
    data(CAMP)

    temp <- genotypeSummary(CAMP)

    print(temp)
    txt(temp, filename="genotypeSummary.txt")
    html(temp, filename="genotypeSummary.html")
    latex(temp, filename="genotypeSummary.tex")

[Package GeneticsBase version 1.0.0 Index]