amAlleleFreq: Determine allele frequencies

In allelematch: Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present

Determine allele frequencies

Description

Determines the allele frequencies for each locus in a multilocus genetic dataset by first removing missing observations. It requires an amDataset object and a map vector relating each column of the dataset to a genetic locus.

Usage

	amAlleleFreq(
		amDatasetFocal, 
		multilocusMap = NULL
		)
		
	## S3 method for class 'amAlleleFreq'
print(x, ...)

Arguments

amDatasetFocal	An amDataset object
multilocusMap	Optionally, a vector of integers or strings giving the mappings onto loci for all genotype columns in amDatasetFocal. When omitted, columns are assumed to be paired (i.e., diploid loci with alleles in adjacent columns). See details.
x	An amDataset object.
...	Additional arguments to summary

Details

This function is called by amUnique.

multilocusMap is often not required, as amDataset objects will typically consist of paired columns of genotypes, where each pair is a separate locus. In cases where this is not the case (e.g., gender is given in only one column), a map vector must be specified.

Example: amDataset consists of gender followed by 4 diploid loci in paired columns
multilocusMap = c(1, 2, 2, 3, 3, 4, 4, 5, 5)
or equally
multilocusMap=c("GENDER", "LOC1", "LOC1", "LOC2", "LOC2", "LOC3", "LOC4", "LOC4")

Value

An amAlleleFreq object

Author(s)

Paul Galpern ([e-mail])

References

For more information and for a complete vignette, please access via the Data S1 Supplementary documentation and tutorials (PDF) located at <doi:10.1111/j.1755-0998.2012.03137.x>.

See Also

amUnique

Examples

	## Not run: 
	data("amExample5")
	
	## Produce amDataset object
	myDataset1 <- 
		amDataset(
			amExample5, 
			missingCode = "-99", 
			indexColumn = 1, 
			metaDataColumn = 2
			)
	
	## Usage
	myAlleleFreq <- 
		amAlleleFreq(
			myDataset1, 
			multilocusMap = c(1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 
			11, 11)
			)
	
	## Produce amDataset object, but remove gender column
	myDataset2 <- 
		amDataset(
			amExample5, 
			missingCode = "-99", 
			indexColumn = 1,
			metaDataColumn = 2, 
			ignoreColumn = "gender"
			)
	
	## Because all columns are paired, usage is simpler
	myAlleleFreq <- amAlleleFreq(myDataset2)
	
## End(Not run)

allelematch documentation built on Aug. 24, 2023, 5:06 p.m.