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.
Value
a data frame with three columns named pos (position of the
differences) and the labels of the two haplotypes compared.
Details
The options strict and trailingGapsAsN are passed to
seg.sites.
# NOT RUN {data(woodmouse)
h <- haplotype(woodmouse)
diffHaplo(h) # compares the 1st and 2nd haplotypesdiffHaplo(h, 1, 3)
diffHaplo(h, "I", "III") # same than above but using labels# }