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 = FALSE, 
                ...)

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 = FALSE
... 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 1.8.0 Index]