freqs2pairwisePi: Calculate pairwise pi between all pairs of individuals in a...
In gbradburd/popgenstuff: Handy Functions for PopGen Analysis in R
Description
Usage
Arguments
Details
Value
Description
Calculate pairwise pi between all pairs of individuals in a dataset
Usage
1
freqs2pairwisePi(freqs, coGeno = NULL, quiet = FALSE)
Arguments
freqs
A genotype matrix with N rows and
L columns, where N is the number
of individuals and L is the number of
loci, for which the i,jth element
gives the frequency of the counted allele in each
individual at each locus.
coGeno
A symmetric matrix (dimensions N x N)
for which the i,jth element gives
the number of base pairs genotyped in both
samples i and j. Default is NULL.
If left unspecified, each cell will be assigned a value of
L (i.e., indicating no missing data).
quiet
A logical value that controls whether
a progress par is displayed. Default is FALSE.
Details
The genotype data should consist of 0,0.5,1
with missing data indicated with NA.
If the genotype matrix consists only of
polymorphic loci, and coGeno either
contains the number of co-genotyped polymorphic
loci for each sample pair or is not specified
this function will return pairwise pi at
polymorphic sites, which may not be
comparable across datasets.
Value
An estimate of pairwise pi between all individuals
in the data matrix.
gbradburd/popgenstuff documentation built on Oct. 16, 2021, 12:05 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value
Description
Calculate pairwise pi between all pairs of individuals in a dataset
Usage
1 | freqs2pairwisePi(freqs, coGeno = NULL, quiet = FALSE)
|
Arguments
freqs |
A genotype matrix with N rows and L columns, where N is the number of individuals and L is the number of loci, for which the i,jth element gives the frequency of the counted allele in each individual at each locus. |
coGeno |
A symmetric matrix (dimensions N x N)
for which the i,jth element gives
the number of base pairs genotyped in both
samples i and j. Default is |
quiet |
A |
Details
The genotype data should consist of 0,0.5,1
with missing data indicated with NA.
If the genotype matrix consists only of
polymorphic loci, and coGeno either
contains the number of co-genotyped polymorphic
loci for each sample pair or is not specified
this function will return pairwise pi at
polymorphic sites, which may not be
comparable across datasets.
Value
An estimate of pairwise pi between all individuals in the data matrix.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.