ContrastSummary: ContrastSummary

In fst4pg: Genetic Distance Segmentation for Population Genetics

ContrastSummary

Description

Summarize multiple Fst profiles

Usage

ContrastSummary(PS, RefLevel, Ratio.thres = 3, NbSnp.min = 1)

Arguments

PS	a list of profile summaries, as provided by the ProfilingSummary function
RefLevel	a list of reference (i.e. baseline) Fst levels
Ratio.thres	a numeric value, regions exhibiting Fst levels whose ratio with the reference level is higher than Ratio.thres will be highlighted.
NbSnp.min	an integer. The minimum number of markers required to highlight a region

Value

a tibble

Examples

## The full example execution takes a few seconds.
# data(Freq);data(NbGamete)
# FreqNbG <- BuildFreqNbG(Freq,NbGamete)
# HFst.m <- HudsonFst.m(FreqNbG)

## Two sets of populations to contrast
# Contrast <- list(America=c("Colombian","Maya"),Europe=c("Tuscan","Italian"))
# Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)
# PS <- ProfilingSummary(Profiles,Info) 

# RefLevel <- rapply(Profiles,median,classes = "numeric",how='list')
# Ratio.thres <- 3
# NbSnp.min <- 1
# CS <- ContrastSummary(PS, RefLevel,
#                       Ratio.thres=Ratio.thres,
#                       NbSnp.min=NbSnp.min)

fst4pg documentation built on July 4, 2022, 1:06 a.m.