ContrastSummary | R Documentation |
Summarize multiple Fst profiles
ContrastSummary(PS, RefLevel, Ratio.thres = 3, NbSnp.min = 1)
PS |
a list of profile summaries, as provided by the |
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 |
a tibble
## 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)
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