checkNullAlleles: Check for potential null (non-amplifying) alleles

In douglasgscofield/readGenalex: Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files

Description

Check genotypes against a set of reference genotypes and look for loci that differ in a way consistent with the occurrence of a null allele, that is, heterozygous in the reference and homozygous matching one of the alleles in the heterozygous reference. A report of genotypes with potential null is generated, unless quiet = TRUE, and a matrix is returned indicating the positions of potential null alleles within the check genotypes. The configuration of this matrix depends on the mode argument.

Usage

checkNullAlleles(ref, check, mode = c("locus", "column"), quiet = FALSE,
  sep = "\t", ...)

Arguments

ref	Object of class genalex containing reference genotypes
check	Object of class genalex containing genotypes to check against ref for possible null alleles
mode	"locus" or "column". Determines containing a potential null allele is indicated in the second index of each element of the return value. If "locus", the value is the locus index, starting from 1. If "column", then the value is the column index within the class genalex data frame.
quiet	Logical. If FALSE, then messages are printed during the check for null alleles in check, and the matrix of potential null allele positions is returned invisibly. If TRUE, then no messages or genotypes are printed, and the matrix of potential null allele positions is returned visibly.
sep	Separator between loci in output, passed to printGenotype
...	Additional parameters passed to printGenotype

Value

A matrix referencing positions within check that contain potential, with its specific format dependent upon the value of mode:

• "locus": a logical matrix having dimensions (attr(check,"n.samples"),attr(check,"n.loci")) and dimnames list(check[,1],attr(check,"locus.names")) with TRUE for each locus in check that might contain a potential null allele

• "column": an integer matrix having dimensions dim(check) and dimnames dimnames(check)) with nonzero values for each position within check that might contain a potential null allele

If quiet = FALSE, this value is returned invisibly.

If quiet = FALSE (the default), output is also written in the form of two messages indicating the number of reference and check genotypes, as well as a listing of specific check and matching reference genotypes with the loci containing the potential null alleles called out. The check and reference genotypes are printed together with a label equal to the respective argument names to indicate their origins. This listing is produced using printGenotype, and arguments can be passed through to modify its output.

Note

The reference genotypes are assumed to be genotyped correctly, without null alleles of their own. The check for null alleles is only as complete as the set of reference genotypes.

Only genotypes with ploidy of 2 are currently supported.

Author(s)

Douglas G. Scofield

See Also

printGenotype

Examples

reffile <- system.file("extdata", "ref_genotypes.txt",
                       package="readGenalex")
checkfile <- system.file("extdata", "check_genotypes.txt",
                         package="readGenalex")
ref <- readGenalex(reffile)
check <- readGenalex(checkfile)
checkNullAlleles(ref, check)

douglasgscofield/readGenalex documentation built on May 15, 2019, 10:43 a.m.