summary.genotype {genetics} | R Documentation |
summary.genotype
creates an object containing allele and
genotype frequency from a genotype
or haplotype
object. print.summary.genotype
displays a
summary.genotype
object.
## S3 method for class 'genotype': summary(object, ..., maxsum) ## S3 method for class 'summary.genotype': print(x,...,round=2)
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. |
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.)
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
.
Gregory R. Warnes warnes@bst.rochester.edu
genotype
,
HWE.test
,
allele
,
homozygote
,
heterozygote
,
carrier
,
allele.count
locus
gene
marker
example.data <- c("D/D","D/I","D/D","I/I","D/D", "D/D","D/D","D/D","I/I","") g1 <- genotype(example.data) g1 summary(g1)