Comparison Between Two Haplotypes

Description

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

Usage

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diffHaplo(h, a = 1, b = 2)

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.

Details

This function prints the number of transitions and transversions between both sequences, and returns a data frame with three columns giving the positions of the differences and the nucleotides in each sequence at these positions.

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

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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

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