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WARNING! This function has been deprecated and is no longer supported. Please use the Differentiation function. A function to calculate differentiation statistics and perform significance testing with a vcf file.

Source: R/Dif_stats.R
Dif_stats.Rd

WARNING! This function has been deprecated and is no longer supported. Please use the Differentiation function. A function to calculate differentiation statistics and perform significance testing with a vcf file.

Usage

Dif_stats(
  VCF,
  pops,
  ploidy,
  statistic = "both",
  boots,
  write = FALSE,
  prefix = NULL
)

Arguments

VCF

Character string indicating the name of the vcf file to be used in analysis.

pops

Character string indicating the name of the population assignment file. This file should have four columns and be in the same order as your vcf file. The first column named Sample indicates the sample name. The second column named Population indicates the population assignment of each individual. The third column named Long indicates the longitude of the sample. The fourth column named Lat indicates the latitude of the sample.

ploidy

Numeric. The ploidy of the data.

statistic

Character string. Options are both, FST, and NeisD.

boots

Numeric. The number of boostraps to use to evaluate statistical significance. Only relevant for FST estimation.

write

Boolean. Whether or not to write the output to a file in the current working directory.

prefix

Character string that will be appended to file output.

Value

A list contianing data frames for the requested statistic.

Examples

# \donttest{
data("HornedLizard_Pop")
data("HornedLizard_VCF")
Test <- Dif_stats(VCF = HornedLizard_VCF, pops = HornedLizard_Pop,
ploidy = 2, statistic = "both", boots = 10, write = FALSE)# }
#> Warning: The Div_Stats function has been deprecated as of PopGenHelpR v1.3.0 and will dissappear in v2.0.0. Please use the Differentiation function if you wish to estimate Fst, Nei's D, or Jost's D.
#> Loading required package: vcfR
#> Registered S3 method overwritten by 'ape':
#>   method   from 
#>   plot.mst spdep
#> 
#>    *****       ***   vcfR   ***       *****
#>    This is vcfR 1.15.0 
#>      browseVignettes('vcfR') # Documentation
#>      citation('vcfR') # Citation
#>    *****       *****      *****       *****
#> Loading required namespace: adegenet
#> Formatting has finished, moving onto calculations
#> Registered S3 method overwritten by 'pegas':
#>   method      from
#>   print.amova ade4