R: Allele and Genotype Frequency from a Genotype or Haplotype...
summary.genotype
R Documentation
Allele and Genotype Frequency from a Genotype or
Haplotype Object
Description
summary.genotype creates an object containing allele and
genotype frequency from a genotype or haplotype
object. print.summary.genotype displays a
summary.genotype object.
Usage
## S3 method for class 'genotype'
summary(object, ..., maxsum)
## S3 method for class 'summary.genotype'
print(x,...,round=2)
Arguments
object, x
an object of class genotype or haplotype (for
summary.genotype) or an object of class
summary.genotype (for print.summary.genotype)
...
optional parameters. Ignored by summary.genotype,
passed to print.matrix by print.summary,genotype.
maxsum
specifying any value for the parameter
maxsum will cause summary.genotype to fall back to
summary.factor.
round
number of digits to use when displaying proportions.
Details
Specifying any value for the parameter maxsum will cause fallback
to summary.factor. This is so that the function
summary.dataframe will give reasonable output when it contains a
genotype column. (Hopefully we can figure out something better to do
in this case.)
Value
The returned value of summary.genotype is an object of class
summary.genotype which
is a list with the following components:
locus
locus information field (if present) from x
.
allele.names
vector of allele names
allele.freq
A two column matrix with one row for each allele, plus one row for
NA values (if present). The first column, Count,
contains the frequency of the corresponding allele value. The
second column, Proportion, contains the fraction of alleles
with the corresponding allele value. Note each observation contains
two alleles, thus the Count field sums to twice the number of
observations.
genotype.freq
A two column matrix with one row for each genotype, plus one row for
NA values (if present). The first column, Count, contains the
frequency of the corresponding genotype. The second column,
Proportion, contains the fraction of genotypes with the
corresponding value.
print.summary.genotype silently returns the object x.