iMKT: integrative MKT method

In sergihervas/iMKT: Integrative McDonald and Kreitman Test

Description

iMKT: MKT using asymptoticMKT method and estimation of negative selection fractions (d, b, f)

Usage

iMKT(daf, divergence, xlow, xhigh, seed, plot = FALSE)

Arguments

daf	data frame containing DAF, Pi and P0 values
divergence	data frame containing divergent and analyzed sites for selected (i) and neutral (0) classes
xlow	lower limit for asymptotic alpha fit
xhigh	higher limit for asymptotic alpha fit
seed	seed value (optional). No seed by default
plot	report plots of daf, alpha and negative selection fractions (optional). Default is FALSE

Details

The integrative MKT (iMKT) allows the estimation of the rate of adaptive evolution (alpha) and the diverse negative selection regimens. iMKT uses asymptotic MKT method (Messer and Petrov 2012 PNAS; Haller and Messer 2017 G3) to estimate alpha and the diverse negative selection fractions (d: strongly deleterious, b: weakly deleterious, f: neutral), based on the assumption that weakly deleterious mutations usually do not reach high allele frequencies and therefore, produce the underestimation of alpha at low DAF categories. The fraction of strongly deleterious mutations is estimated as the difference between neutral (0) and selected (i) polymorphic sites relative to the number of analyzed sites: d = 1 - (P0/m0 / Pi/mi). The fraction of weakly deleterious sites (b) corresponds to the relative proportion of selected polymorphic sites that cause the underestimation of alpha at low DAF categories. Finally, the fraction of neutral sites (f) is estimated as: f = 1 - d - b. iMKT() only fits an exponential model for the computation of alpha.

Value

iMKT method. List with asymptotic MK table and values, fractions of sites and graphs of DAF, asymptotic alpha model and negative selection fractions (optional).

Examples

## Without plot
iMKT(myDafData, myDivergenceData, xlow=0, xhigh=0.9)
## With plot
iMKT(myDafData, myDivergenceData, xlow=0, xhigh=0.9, plot=TRUE)

sergihervas/iMKT documentation built on May 3, 2019, 1:49 p.m.