amAlleleFreq {allelematch} | R Documentation |
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 |
multilocusMap |
Optionally, a vector of integers or strings giving the mappings onto loci for all
genotype columns in |
x |
An |
... |
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 (pgalpern@gmail.com)
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
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)