summary.haplo.em: Summarize contents of a haplo.em object

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Summarize contents of a haplo.em object

Description

Display haplotype pairs and their posterior probabilities by subject. Also display a table with number of max haplotype pairs for a subject versus how many were kept (max vs. used).

Usage

## S3 method for class 'haplo.em'
summary(object, show.haplo=FALSE, digits=max(options()$digits-2, 5), nlines=NULL, ...)

Arguments

object	A haplo.em object
show.haplo	Logical. If TRUE, show the alleles of the haplotype pairs, otherwise show only the recoded values.
digits	number of significant digits to be printed for numeric values
nlines	To shorten output, print the first 1:nlines rows of the large data frame.
...	Optional arguments for the summary method

Value

A data.frame with a row for every subject's possible haplotype pairs and the posterior probabilities of that pair given their genotypes.

See Also

haplo.em

Examples

data(hla.demo)
geno <- hla.demo[,c(17,18,21:24)]
label <-c("DQB","DRB","B")
keep <- !apply(is.na(geno) | geno==0, 1, any)

save.em.keep <- haplo.em(geno=geno[keep,], locus.label=label)
save.df <- summary(save.em.keep)
save.df[1:10,]

haplo.stats documentation built on May 29, 2024, 9:53 a.m.