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Fis filter

Source: R/filter_fis.R
filter_fis.Rd

Filter markers or loci using within-stratum inbreeding-coefficient statistics.

Filter target: Markers or loci, depending on approach.

Usage

filter_fis(
  data,
  approach = "haplotype",
  fis.min.threshold,
  fis.max.threshold,
  fis.diff.threshold,
  pop.threshold,
  percent,
  filename,
  verbose = TRUE
)

Arguments

data

A GDS filename or open SeqVarGDSClass object.

approach

Character. By "SNP" or by "haplotype". The function will consider the SNP or haplotype statistics to filter the marker. Default: approach = "haplotype".

fis.min.threshold

Number.

fis.max.threshold

Number.

fis.diff.threshold

Number (0 - 1)

pop.threshold

Fixed number of pop required to keep the locus.

percent

Is the threshold a percentage ? TRUE or FALSE.

filename

(optional) The function uses write.fst, to write the tidy data frame in the folder created in the working directory. The file extension appended to the filename provided is .rad.

verbose

Logical. Display progress messages. Default: verbose = TRUE.

Details

The Fis calculated uses the ratio of averages (1-mean(Ho)/mean(Hs)) and NOT THE AVERAGE OF RATIOS (Nei 1987).

References

Nei M. (1987) Molecular Evolutionary Genetics. Columbia University Press.

Author

Thierry Gosselin thierrygosselin@icloud.com