Formal class "SNPbin"
The class SNPbin is a formal (S4) class for storing a genotype
of binary SNPs in a compact way, using a bit-level coding scheme.
This storage is most efficient with haploid data, where the memory
taken to represent data can reduced more than 50 times. However,
SNPbin can be used for any level of ploidy, and still remain an
efficient storage mode.
A SNPbin object can be constructed from
a vector of integers giving the number of the second allele for each
locus.
SNPbin stores a single genotype. To store multiple genotypes,
use the genlight class.
SNPbin objects can be created by calls to new("SNPbin",
...), where '...' can be the following arguments:
snpa vector of integers or numeric giving numbers of copies of the second alleles for each locus. If only one unnamed argument is provided to 'new', it is considered as this one.
ploidyan integer indicating the ploidy of the genotype; if not provided, will be guessed from the data (as the maximum from the 'snp' input vector).
labelan optional character string serving as a label for the genotype.
The following slots are the content of instances of the class
SNPbin; note that in most cases, it is better to retrieve
information via accessors (see below), rather than by accessing the
slots manually.
snp:a list of vectors with the class raw.
n.loc:an integer indicating the number of SNPs of the genotype.
NA.posi:a vector of integer giving the position of missing data.
label:an optional character string serving as a label for the genotype..
ploidy:an integer indicating the ploidy of the genotype.
Here is a list of methods available for SNPbin objects. Most of
these methods are accessors, that is, functions which are used to
retrieve the content of the object. Specific manpages can exist for
accessors with more than one argument. These are indicated by a '*'
symbol next to the method's name. This list also contains methods
for conversion from SNPbin to other classes.
signature(x = "SNPbin"): usual method to subset
objects in R. The argument indicates how SNPs are to be
subsetted. It can be a vector of signed integers or of logicals.
signature(x = "SNPbin"): printing of the
object.
signature(x = "SNPbin"): similar to the @ operator;
used to access the content of slots of the object.
signature(x = "SNPbin"): similar to the @ operator;
used to replace the content of slots of the object.
signature(x = "SNPbin"): returns the number of
SNPs in the object.
signature(x = "SNPbin"): returns the names of
the slots of the object.
signature(x = "SNPbin"): returns the ploidy of
the genotype.
signature(x = "SNPbin"): converts a
SNPbin object to a vector of integers. The S4 method 'as' can
be used as well (e.g. as(x, "integer")).
signature(x = "SNPbin"): merges genotyping of
the same individual at different SNPs (all stored as
SNPbin objects) into a single SNPbin.
signature(x = "SNPbin"): same as cbind.SNPbin.
Thibaut Jombart (t.jombart@imperial.ac.uk)
## Not run:
#### HAPLOID EXAMPLE ####
## create a genotype of 100,000 SNPs
dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE)
dat[1:10]
x <- new("SNPbin", dat)
x
x[1:10] # subsetting
as.integer(x[1:10])
## try a few accessors
ploidy(x)
nLoc(x)
head(x$snp[[1]]) # internal bit-level coding
## check that conversion is OK
identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE
## compare the size of the objects
print(object.size(dat), unit="auto")
print(object.size(x), unit="auto")
object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
#### TETRAPLOID EXAMPLE ####
## create a genotype of 100,000 SNPs
dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE)
x <- new("SNPbin", dat)
identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE
## compare the size of the objects
print(object.size(dat), unit="auto")
print(object.size(x), unit="auto")
object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
#### c, cbind ####
a <- new("SNPbin", c(1,1,1,1,1))
b <- new("SNPbin", c(0,0,0,0,0))
a
b
ab <- c(a,b)
ab
identical(c(a,b),cbind(a,b))
as.integer(ab)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.