Description Usage Arguments Value Note Author(s) See Also Examples
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.
1 2 |
ref |
Object of class |
check |
Object of class |
mode |
|
quiet |
Logical. If |
sep |
Separator between loci in output, passed to
|
... |
Additional parameters passed to |
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.
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.
Douglas G. Scofield
1 2 3 4 5 6 7 | 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)
|
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