R: Comparison Between Two Haplotypes

diffHaplo {pegas} | R Documentation

## Comparison Between Two Haplotypes

### Description

This function compares two haplotypes and returns a summary of the differences.

### Usage

    diffHaplo(h, a = 1, b = 2, strict = FALSE, trailingGapsAsN = TRUE)

### Arguments

`h` | an object of class `"haplotype"`.
`a, b` | two integers (or character strings) giving the indices (or labels) of the two haplotypes to be compared.
`strict` | a logical value; if `TRUE`, ambiguities and gaps in the sequences are ignored and treated as separate characters.
`trailingGapsAsN` | a logical value; if `TRUE` (the default), the leading and trailing alignment gaps are considered as unknown bases (i.e., N). This option has no effect if `strict = TRUE`.

### Details

The options `strict` and `trailingGapsAsN` are passed to `seg.sites`.

### Value

a data frame with three columns named `pos` (position of the differences) and the labels of the two haplotypes compared.

### Author(s)

Emmanuel Paradis

### See Also

`haploNet`, `haplotype`

### Examples

    data(woodmouse)
    h <- haplotype(woodmouse)
    diffHaplo(h) # compares the 1st and 2nd haplotypes
    diffHaplo(h, 1, 3)
    diffHaplo(h, "I", "III") # same than above but using labels

[Package pegas version 1.1 Index]