AnalyseSplittedExpt: A function to analyse a selection experiment, including...
In laurentlab-mpipz/rsurvival: Process genotype data from survival experiment

Description Usage Arguments Value See Also Examples

A function to analyse a selection experiment, including observed frequencies of genotype and probabilities that they are due to random picking and positive selection.

AnalyseSplittedExpt(gt.alive, gt.dead, min.freq.al = NULL,
  location.cols = TRUE, deltas = TRUE, p.values = TRUE,
  genotypic = FALSE, gt.pop1 = NULL, gt.pop2 = NULL,
  backup.path = NULL)

`gt.alive`	A genotype data frame of the alive population
`gt.dead`	A genotype data frame of the dead population
`min.freq.al`	Optional. Numeric from 0 to 1. Variants with MAF under this threshold will be ommited.
`location.cols`	If TRUE, adds two columns to the result, which are the scaffold name and the locus name as factors (deafult is FALSE)
`deltas`	If TRUE (default), include columns of differencies between relative allelic frequencies after selection and before selection in the result. Positive value means that the allele is more common in the survivers population.
`p.values`	If TRUE (default), some probabilities will be included in the result, as well as frequencies
`genotypic`	If TRUE, will include counts of genotype in the result.
`gt.pop1`	Optional. A genotype matrix. If both `gt.pop1` and `gt.pop2` are set, will include the W&C FST estimation to the result.
`gt.pop2`	Optional. A genotype matrix. If both `gt.pop1` and `gt.pop2` are set, will include the W&C FST estimation to the result.
`backup.path`	Optionnal. A path where backup files can be stored

A data frame of frequencies and probabilities from your experiment.

For more information, see CalcProbsSelection and CalcFreqGt which this function bind.

## Not run: 
AnalyseSplittedExpt(gt.alive, gt.dead)
AnalyseSplittedExpt(gt.alive, gt.dead, min.freq.al = 0.1)
AnalyseSplittedExpt(gt.alive, gt.dead, location.cols = FALSE)
AnalyseSplittedExpt(gt.alive, gt.dead, deltas = FALSE, p.values = FALSE)
AnalyseSplittedExpt(gt.alive, gt.dead, backup.path = "example.csv")

## End(Not run)