Overview
iMKT is an R package that includes all the features used in this web server to compute the McDonald and Kreitman test from different methodologies. The package can be used on polymorphism and divergence genomic data provided by the user or automatically downloaded from PopFly (Hervas et al. 2017) or PopHuman (Casillas et al. 2018). It includes four MK derived methodologies which allow inferring the rate of adaptive evolution (α) as well as other selective regimes, including the fraction of strongly deleterious (d), weakly deleterious (b), and neutral (f) sites.
Installation
The package is deposited in GitHub and can be installed using the devtools library.
## Install devtools package, if necessary
install.packages("devtools" )
## Install iMKT package from GitHub repository
devtools::install_github("sergihervas/iMKT")
## Load iMKT library
library(iMKT)
Usage
In summary, iMKT allows performing diverse MK-derived tests using the number of polymorphic (P, classified in Derived Allele Frequency (DAF) categories), divergent (D) and analyzed (m) sites for putatively neutral (0) and putatively selected (i) sites. Briefly, most functions require two input parameters: daf (data frame containing DAF, Pi and P0) and divergence (data frame containing mi, Di, m0, D0) and return the estimation of α together with specific details of the methodology.
The package includes two sample data frames (myDafData, myDivergenceData). The vignettes and manual documentation contain detailed descriptions and examples of each function and type of analysis, and instructions on how to use PopFly and PopHuman genomic data.
## Sample daf data included in the package
head(myDafData)
daf Pi P0
1 0.025 22490 17189
2 0.075 3217 4780
3 0.125 1616 2874
4 0.175 999 2088
5 0.225 754 1685
6 0.275 679 1443
## Sample divergence data included in the package
myDivergenceData
mi Di m0 D0
1 2598805 54641 620019 52537
## Perform standard MKT
standardMKT(myDafData, myDivergenceData)
$alpha.symbol
[1] 0.2364499
$`Fishers exact test P-value`
[1] 1.480943e-183
$`MKT table`
| | Polymorphism| Divergence|
|:--------------|------------:|----------:|
|Neutral class | 45101| 52537|
|Selected class | 35816| 54641|
$`Divergence metrics`
| Ka| Ks| omega| omegaA| omegaD|
|---------:|---------:|---------:|--------:|--------:|
| 0.0210254| 0.0847345| 0.2481331| 0.058671| 0.189462|
Development
iMKT has been developed by Sergi Hervás (sergi.hervas@uab.cat), Marta Coronado (marta.coronado@uab.cat) and Jesús Murga (jesus.murga@uab.cat), from the Bioinformatics of Genomics Diversity group from the Universitat Autònoma de Barcelona (UAB) and the Institut de Biotecnologia i Biomedicina (IBB).
If you have any feedback or feature requests regarding iMKT, please contact antonio.barbadilla@uab.cat or jesus.murga@uab.cat.