Haplotype Frequencies With a Covariate
This utility function extracts the absolute frequencies of haplotypes with respect to a categorical variable (a factor). The output is useful when ploting haplotype networks.
haploFreq(x, fac, split = "_", what = 2, haplo = NULL)
x |
a set of DNA sequences (as an object of class
|
fac |
a factor giving the categorical variable (can be missing). |
split |
a single character (see details). |
what |
a single integer (see details). |
haplo |
an object of class |
The frequencies of each haplotype in x are counted with respect
to a factor which is either specified with fac, or extracted
from the labels of x. In the second case, these labels are
split with respect to the character specified in split and the
what'th substrings are extracted and taken as the categorical
variable (see example).
If haplo is specified, the haplotype frequencies are taken from
it, otherwise they are calculated from x.
a matrix of counts.
Klaus Schliep and Emmanuel Paradis
## generate some artificial data from 'woodmouse':
data(woodmouse)
x <- woodmouse[sample(15, size = 50, replace = TRUE), ]
## labels IdXXX_PopXXX_LocXXX
rownames(x) <- paste("Id", 1:50, "_Pop", 1:2, "_Loc", 1:5, sep = "")
head(labels(x))
h <- haplotype(x)
## frequencies of haplotypes wrt 'Pop':
f.pop <- haploFreq(x, haplo = h)
## frequencies of haplotypes wrt 'Loc':
f.loc <- haploFreq(x, what = 3, haplo = h)
nt <- haploNet(h)
fq <- attr(nt, "freq")
op <- par(mfcol = c(1, 2))
plot(nt, size = fq, pie = f.pop, labels = FALSE)
plot(nt, size = fq, pie = f.loc, labels = FALSE)
par(op)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.