R: Summarize contents of a haplo.em object

summary.haplo.em {haplo.stats} | R Documentation

## 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,]

[Package haplo.stats version 1.7.9 Index]