haplotype: Haplotype Extraction and Frequencies

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/haplotype.R

Description

haplotype extracts the haplotypes from a set of DNA sequences. The result can be plotted with the appropriate function.

Usage

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haplotype(x, ...)
## S3 method for class 'DNAbin'
haplotype(x, labels = NULL, ...)
## S3 method for class 'character'
haplotype(x, labels = NULL, ...)
## S3 method for class 'numeric'
haplotype(x, labels = NULL, ...)
## S3 method for class 'haplotype'
plot(x, xlab = "Haplotype", ylab = "Number", ...)
## S3 method for class 'haplotype'
print(x, ...)
## S3 method for class 'haplotype'
sort(x,
     decreasing = ifelse(what == "frequencies", TRUE, FALSE),
     what = "frequencies", ...)
## S3 method for class 'haplotype'
x[...]

Arguments

x

a set of DNA sequences (as an object of class "DNAbin"), or an object of class "haplotype".

labels

a vector of character strings used as names for the rows of the returned object. By default, Roman numerals are given.

xlab, ylab

labels for the x- and x-axes.

...

further arguments passed to barplot (unused in print and sort).

decreasing

a logical value specifying in which order to sort the haplotypes; by default this depends on the value of what.

what

a character specifying on what feature the haplotypes should be sorted: this must be "frequencies" or "labels", or an unambiguous abbreviation of these.

Details

The sort method sorts the haplotypes in decreasing frequencies (the default) or in alphabetical order of their labels (if what = "labels"). Note that if these labels are Roman numerals (as assigned by haplotype), their alphabetical order may not be their numerical one (e.g., IX is alphabetically before VIII).

From pegas 0.7, haplotype extracts haplotypes taking into account base ambiguities.

Value

haplotype returns an object of class c("haplotype", "DNAbin") which is an object of class "DNAbin" with two additional attributes: "index" identifying the index of each observation that share the same haplotype, and "from" giving the name of the original data.

sort returns an object of the same class respecting its attributes.

Author(s)

Emmanuel Paradis

See Also

haploNet, haploFreq, subset.haplotype, DNAbin for manipulation of DNA sequences in R.

The haplotype method for objects of class "loci" is documented separately: haplotype.loci.

Examples

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## generate some artificial data from 'woodmouse':
data(woodmouse)
x <- woodmouse[sample(15, size = 110, replace = TRUE), ]
(h <- haplotype(x))
## the indices of the individuals belonging to the 1st haplotype:
attr(h, "index")[[1]]
plot(sort(h))
## get the frequencies in a named vector:
setNames(lengths(attr(h, "index")), labels(h))

pegas documentation built on July 13, 2018, 1:02 a.m.