Estimate \(\beta\)s per population.
betas_estimator(data, strata = NULL, filename = NULL, verbose = FALSE)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.
(optional)
The strata file is a tab delimited file with a minimum of 2 columns headers:
INDIVIDUALS and STRATA. Documented in read_strata.
DArT data: a third column TARGET_ID is required.
Documented on read_dart. Also use the strata read function to
blacklist individuals.
Default: strata = NULL.
(optional) The function uses write.fst,
to write the tidy data frame in
the working directory. The file extension appended to
the filename provided is .rad.
With default: filename = NULL, the tidy data frame is
in the global environment only (i.e. not written in the working directory...).
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE.
A list is created with 3 objects: betaiovl: Average \(\beta_i\) over loci, Hw: Within population gene diversities Hb: Between populations gene diversities
Weir, B., Goudet, J. (2017). A Unified Characterization of Population Structure and Relatedness Genetics 206(4), 2085-2103. https://dx.doi.org/10.1534/genetics.116.198424
Goudet, J., Kay, T., Weir, B. (2018). How to estimate kinship Molecular Ecology 27(20), 4121-4135. https://dx.doi.org/10.1111/mec.14833
if (FALSE) { # \dontrun{
# Using a VCF file, the simplest for of the function:
fh <- ibdg_fh(
data = "batch_1.vcf",
strata = "strata.panda.tsv"
)
# To see what's inside the list
names(fh)
# To view the manhattan plot:
fh$fh.manhattan.plot
# To view the distribution of FH values:
fh$fh.distribution.plot
} # }