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Integrative McDonald and Kreitman test

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imkt's Introduction

iMKT: integrative McDonald and Kreitman Test

Overview

iMKT is an R package to compute the McDonald and Kreitman test (McDonald and Kreitman 1991 Nature) on polymorphism and divergence genomic data provided by the user or automatically downloaded from PopFly (Hervas et al. 2017 Bioinformatics) or PopHuman (Casillas et al. 2018 Nucleic Acids Res.). It includes five MK derived methodologies which allow inferring the rate of adaptive evolution (α) as well as 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
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 neutral (0) and selected (i) classes. 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.

The following example, which shows how to perform a standard MK test using sample data, is aimet at illustrating how the iMKT package works.

## 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|

Citation

Citation to paper

Licence

Licence of package

Development & Contact

iMKT has been developed by Sergi Hervas ([email protected]), Marta Coronado ([email protected]) and Jesús Murga ([email protected]), from the Bioinformatics of Genome 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 [email protected] or [email protected].

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soniacasillas bgd-uab salejandro edison2021

imkt's Issues

PopFlyAnalysis() producing empty list as output

Hello-

I am having an issue with the function PopFlyAnalysis(). It runs without error, but just produces an empty list as output. For example, for the gene FBgn0000008 in population RAL, I'm trying to run:

PopFlyAnalysis(genes = c("FBgn0000008"), pops = "RAL", recomb = FALSE, test = "FWW", plot = FALSE)

And here's what the output looks like:

If I try to assign the output to a variable instead:
output = PopFlyAnalysis(genes = c("FBgn0000008"), pops = "RAL", recomb = FALSE, test = "FWW", plot = FALSE)
I get:

I'm not sure what the issue is; any insight/advice would be much appreciated.

Thanks!
Alissa

multipleDatasets()

remove function

Problems running iMKT R code

Hi,

I was trying to use iMKT example data and I keep getting errors when using the PopHumanAnalysis() or PopFlyAnalysis() functions. For example, if I run the following example data in the vignette:

> loadPopFly()
Loading PopFly data into your workspace.
This process may take several seconds to complete, please be patient.
> ls()
[1] "data"         "genes"        "my_pops"      "mygenes"      "PopFlyData"   "PopHumanData"
> names(PopFlyData)
 [1] "Name"  "Pop"   "DAF0f" "DAF4f" "p0"    "pi"    "di"    "d0"    "Chr"   "mi"    "m0"    "cM_Mb"
> PopFlyAnalysis(genes=c("FBgn0000055","FBgn0003016"), pops=c("RAL","ZI"), recomb=F, test="DGRP", plot=TRUE)

list()
Warning messages:
1: In length(genes) == 0 || genes == "" :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
2: In length(pops) == 0 || pops == "" :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

Running the examples from the functions also triggers the same error:

> mygenes <- c("FBgn0053196", "FBgn0086906", "FBgn0261836", "FBgn0031617", 
+                           "FBgn0260965", "FBgn0028899", "FBgn0052580", "FBgn0036181",
+                           "FBgn0263077", "FBgn0013733", "FBgn0031857", "FBgn0037836")
> ## Perform analyses
> PopFlyAnalysis(genes=mygenes, pops="RAL", recomb=FALSE, test="iMKT", xlow=0, xhigh=0.9, plot=TRUE)

list()
Warning message:
In length(genes) == 0 || genes == "" :
  'length(x) = 12 > 1' in coercion to 'logical(1)'

The PopHumanData has the same issue, and doesn't even recognize the populations specified in the example itself:

> loadPopHuman()
Loading PopHuman data into your workspace.
This process may take several seconds to complete, please be patient.
> ls()
[1] "data"         "genes"        "my_pops"      "mygenes"      "PopFlyData"   "PopHumanData"
> names(PopHumanData)
 [1] "ID"       "chr"      "pop"      "pi"       "p0"       "DAF0f"    "DAF4f"    "mi"       "m0"       "di"       "d0"      
[12] "symbol"   "recomb"   "globalID"
> mygenes <- c("ENSG00000011021.21_3","ENSG00000091483.6_3","ENSG00000116191.17_3",
+              "ENSG00000116337.15_4","ENSG00000116584.17_3","ENSG00000116745.6_3",
+              "ENSG00000116852.14_3","ENSG00000116898.11_3","ENSG00000117010.15_3",
+              "ENSG00000117090.14_3","ENSG00000117222.13_3","ENSG00000117394.20_3")
> ## Perform analyses
> PopHumanAnalysis(genes=mygenes , pops=c("CEU","YRI"), recomb=FALSE, test="standardMKT")
Error in PopHumanAnalysis(genes = mygenes, pops = c("CEU", "YRI"), recomb = FALSE,  : 
  MKT data is not available for the sequested populations(s).
Select among the following populations:
ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD, IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, YRI!.
The populations that caused the error are: .
In addition: Warning messages:
1: In length(genes) == 0 || genes == "" :
  'length(x) = 12 > 1' in coercion to 'logical(1)'
2: In length(pops) == 0 || pops == "" :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

I believe part of the issue is related to some change in R where you can no longer combine && or || with length arguments as explained here.

I also noticed that none of the tutorials in the iMKT website work, since I always get the following warning:
A minimum number of segregating sites is needed to run an asymptotic MKT. Please add more genes to the analysis or change the MKT extension.

Not sure if this is related, but thought I would also point it out.

Thank you,
Mafalda

Recombination from Comeron et al. (reference)
Include report recomb bins (numer genes, mean values, etc)

Plots iMK

Change order: 1) DAF 2) alpha 3) Fractions

rename functions

check_input --> checkInput
theme_publication --> themePublication

consistency and vignettes pdf output.