pwp2allelicCov | R Documentation |
pwp2allelicCov
converts a measures of
pairwise pi to allelic covariance
pwp2allelicCov(pi)
pi |
A measurement of nucleotide diversity between
a pair of samples; it is the proportion of sites at which
the samples differ, out of the total number of loci
in the sample. Can be a single value, a |
This function takes measurements of pairwise pi and returns the allelic covariance, which can then be used in a BEDASSLE analysis.
This function takes a measurement or set of measurements
of pairwise pi between samples and converts it to a an
allelic covariance, which can then be used to run a
run.bedassle
analysis. The pi
argument
specified will most commonly be a matrix
of pairwise pi
between a set of samples, for which the ijth cell gives
the pairwise pi between samples i and j. However,
it will also convert a single value (i.e., pairwise pi between
a single pair of samples) or a vector of values.
Pairwise pi is calculated as the proportion of sites at which a pair of samples differs out of the total number of loci in the dataset. If it is calculated using only loci that are polymorphic in the global dataset, it is called pi at polymorphic sites. If it is calculated using all genotyped base-pairs, it is simply pi. Either statistic can be converted to allelic covariance and used for running BEDASSLE.
This function returns the allelic covariance that corresponds to
a particular value of pairwise pi. The allelic covariance can then be
used to run a BEDASSLE analysis run with run.bedassle
.
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