Summarize contents of a haplo.em object

Share:

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

1
2
## 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

1
2
3
4
5
6
7
8
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,]

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.