TODO
filter_fis(
data,
approach = "haplotype",
fis.min.threshold,
fis.max.threshold,
fis.diff.threshold,
pop.threshold,
percent,
filename
)14 options for input (diploid data only): VCFs (SNPs or Haplotypes,
to make the vcf population ready),
plink (tped, bed), stacks haplotype file, genind (library(adegenet)),
genlight (library(adegenet)), gtypes (library(strataG)), genepop, DArT,
and a data frame in long/tidy or wide format. To verify that radiator detect
your file format use detect_genomic_format (see example below).
Documented in Input genomic datasets of tidy_genomic_data.
DArT and VCF data: radiator was not meant to generate alleles and genotypes if you are using a VCF file with no genotype (only genotype likelihood: GL or PL). Neither is radiator able to magically generate a genind object from a SilicoDArT dataset. Please look at the first few lines of your dataset to understand it's limit before asking raditor to convert or filter your dataset.
Character. By "SNP" or by "haplotype".
The function will consider the SNP or haplotype statistics to filter the marker.
Default by "haplotype".
Number.
Number.
Number (0 - 1)
Fixed number of pop required to keep the locus.
Is the threshold a percentage ? TRUE or FALSE.
(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.
Default: filename = NULL.
The Fis calculated uses the ratio of averages (1-mean(Ho)/mean(Hs)) and NOT THE AVERAGE OF RATIOS (Nei 1987).
Nei M. (1987) Molecular Evolutionary Genetics. Columbia University Press.