PopHumanAnalysis: iMKT using PopHuman data

In sergihervas/iMKT: Integrative McDonald and Kreitman Test

Description

Perform any MKT method using a subset of PopHuman data defined by custom genes and populations lists

Usage

PopHumanAnalysis(genes = c("gene1", "gene2", "..."), pops = c("pop1",
  "pop2", "..."), cutoffs = c(0, 0.05, 0.1), recomb = TRUE/FALSE,
  bins = 0, test = c("standardMKT", "DGRP", "FWW", "asymptoticMKT",
  "iMKT"), xlow = 0, xhigh = 1, plot = FALSE)

Arguments

genes	list of genes to analyze
pops	list of populations to analyze
cutoffs	list of cutofs to perform FWW and/or DGRP
recomb	group genes according to recombination values (TRUE/FALSE)
bins	number of recombination bins to compute (mandatory if recomb=TRUE)
test	which test to perform. Options include: standardMKT (default), DGRP, FWW, asymptoticMKT, iMKT
xlow	lower limit for asymptotic alpha fit (default=0)
xhigh	higher limit for asymptotic alpha fit (default=1)
plot	report plot (optional). Default is FALSE

Details

Execute any MKT method (standardMKT, FWW, DGRP, asymptoticMKT, iMKT) using a subset of PopHuman data defined by custom genes and populations lists. It uses the dataframe PopHumanData, which can be already loaded in the workspace (using loadPopHuman()) or is directly loaded when executing this function. It also allows deciding whether to analyze genes groupped by recombination bins or not, using recombination rate values corresponding to the sex average estimates from Bh<c3><a9>rer et al. 2017 Nature Commun.

Value

List of lists with the default test output for each selected population (and recombination bin when defined)

Examples

## List of genes
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")
PopHumanAnalysis(genes=mygenes , pops=c("CEU"), recomb=TRUE, bins=3, test="DGRP")

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