Description Usage Arguments Details Value Examples
View source: R/PopFlyAnalysis.R
Perform any MKT method using a subset of PopFly data defined by custom genes and populations lists
1 2 3 4 |
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 |
Execute any MKT method (standardMKT, FWW, DGRP, asymptoticMKT, iMKT) using a subset of PopFly data defined by custom genes and populations lists. It uses the dataframe PopFlyData, which can be already loaded in the workspace (using loadPopFly()) 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 estimates from Comeron et al. 2012 Plos Genetics.
List of lists with the default test output for each selected population (and recombination bin when defined)
1 2 3 4 5 6 7 | ## List of genes
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)
PopFlyAnalysis(genes=mygenes, pops=c("RAL","ZI"), recomb=TRUE, bins=3, test="DGRP", plot=FALSE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.