HudsonFst.prof {fst4pg}

HudsonFst.prof

Description

Perform FST profiling between pairs of pops, as requested by Contrast. If no contrast is provided, all pairs are considered

Usage

HudsonFst.prof(
  HFst.m,
  Contrast = NULL,
  Kmax = 100,
  NbSegCrit = "biggest.S3IB",
  parallel = TRUE
)

Arguments

HFst.m

A list of data.frame with two columns each, Fst and Weight, as provided by the HudsonFst.m function

Contrast

a list of two vectors with the names of the populations to be contrasted

Kmax

maximum number of breakpoints to be considered

NbSegCrit

the criterion used for the choice of the number of segments

parallel

a boolean, should the profiling be parallelized (using future) or not

Value

a smoothed profile

Examples

data(Freq);data(NbGamete)
FreqNbG <- BuildFreqNbG(Freq,NbGamete)
HFst.m <- HudsonFst.m(FreqNbG)

## Two population analysis
TwoPops <- list(First="Colombian",Second="Tuscan")
HFst.prof <- HudsonFst.prof(HFst.m,Contrast=TwoPops)

## The full example execution takes a few seconds.
## Two sets of populations to contrast

Contrast <- list(America=c("Colombian","Maya"),Europe=c("Tuscan","Italian"))
Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)

## For larger lists and/or larger marker sets, 
## use the future package for parallel computation:

future::plan("multisession",workers=4)
Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)
future::plan("default")