callGenotypes: Make genotype calls
In mlgt: Multi-Locus Geno-Typing

Description Usage Arguments Details Value Examples

Apply a genotype call method to a table or list of tables of variant data such as the markerSampleList table of an mlgtResult.

  callGenotypes(resultObject,
    method = "callGenotypes.default",
    markerList = names(resultObject@markers),
    sampleList = resultObject@samples, mapAlleles = FALSE,
    alleleDb = NULL, approxMatching = FALSE, ...)

`resultObject`	An object of class `mlgtResult`, as returned by `mlgt`
`alleleDb`	A list of `variantMap` objects derived from known alleles. As made by `createKnownAlleleList`
`method`	How to call genotypes. Currently only "callGenotypes.default" is implemented. Users can define their own methods as R functions (see the vignette).
`markerList`	For which of the markers do you want to call genotypes (default is all)?
`sampleList`	For which of the samples do you want to call genotypes (default is all)?
`mapAlleles`	FALSE/TRUE. Whether to map variants to db alleleDb of known alleles.
`approxMatching`	If TRUE, a BLAST search is also performed to find matches (slower). Additional columns are added to the genoytpeTable
`...`	Other parameter values will be passed to custom methods such as `callGenotypes.default`

After mlgt has generated tables of the most common variants assigned in each marker/sample pair, an attempt can be made to call genotypes. This is kept separate because users might want to try different calling methods and have the option to map to a known set of alleles. Currently, only one method is implemented (‘custom’). See callGenotypes.default. This function also includes the option to map variants to a list of known alleles created using createKnownAlleleList. The basic method makes only perfect matches but a secondary method can be triggered (approxMatching=TRUE) to find the allele with the greatest similarity using a local BLAST search.

list of call results including the call parameters and a table of calls (class genotypeCall). If an mlgtResult object was supplied then a list of genotypeCall objects will be returned, each named by marker.

## Not run: 
data("mlgtResult", package="mlgt")
my.mlgt.Result
# the default method
my.genoytpes <- callGenotypes(my.mlgt.Result)
# using a custom method
callGenotypes.custom <- function(table, maxPropUniqueVars=0.5) {
	table$status <- "notCalled"
	table$propUniqueVars <- table$numbVar/table$numbSeq
	table$status <- ifelse(table$propUniqueVars <= maxPropUniqueVars,"good", "bad")
	return(table)
}
my.custom.Genotypes <- callGenotypes(my.mlgt.Result, method="callGenotypes.custom")

## End(Not run)