calcThetaW: Calculate Wu and Watterson's Theta
In gbradburd/popgenstuff: Handy Functions for PopGen Analysis in R
Description
Usage
Arguments
Details
Value
Description
Calculate Wu and Watterson's Theta
Usage
1
calcThetaW(gt, lociDistn = NULL)
Arguments
gt
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 number of the counted allele in each
individual at each locus.
lociDistn
A vector of length N,
for which the ith element
gives the number of base pairs genotyped in exactly
i individuals. E.g., the 3rd element of
lociDistn gives the number of base pairs
genotyped in exactly 3 individuals. Default is
NULL.
Details
The data matrix gt should consist of
0s, 1s, and 2s, with missing data indicated with
NA. This can be generated from a VCF file
using vcf2R, and the lociDistn
can be generated using getBPstats.
If lociDistn is not specified,
and gt consists only of polymorphic
loci, this function will return Wu and
Watterson's Theta at polymorphic sites,
which may not be comparable across datasets.
Value
An estimate of Wu and Watterson's Theta.
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 Wu and Watterson's Theta
Usage
1 | calcThetaW(gt, lociDistn = NULL)
|
Arguments
gt |
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 number of the counted allele in each individual at each locus. |
lociDistn |
A vector of length N,
for which the ith element
gives the number of base pairs genotyped in exactly
i individuals. E.g., the 3rd element of
|
Details
The data matrix gt should consist of
0s, 1s, and 2s, with missing data indicated with
NA. This can be generated from a VCF file
using vcf2R, and the lociDistn
can be generated using getBPstats.
If lociDistn is not specified,
and gt consists only of polymorphic
loci, this function will return Wu and
Watterson's Theta at polymorphic sites,
which may not be comparable across datasets.
Value
An estimate of Wu and Watterson's Theta.
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.