Description Usage Arguments Details Value Author(s) Examples
Accessors for slots in gtypes objects.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | ## S4 method for signature 'gtypes'
getNumInd(x, by.strata = FALSE, ...)
## S4 method for signature 'gtypes'
getNumLoci(x, ...)
getNumStrata(x, ...)
## S4 method for signature 'gtypes'
getNumStrata(x, ...)
getIndNames(x, ...)
## S4 method for signature 'gtypes'
getIndNames(x, by.strata = FALSE, ...)
getLociNames(x, ...)
## S4 method for signature 'gtypes'
getLociNames(x, ...)
getAlleleNames(x, ...)
## S4 method for signature 'gtypes'
getAlleleNames(x, ...)
getStrataNames(x, ...)
## S4 method for signature 'gtypes'
getStrataNames(x, ...)
getPloidy(x, ...)
## S4 method for signature 'gtypes'
getPloidy(x, ...)
getStrata(x, ...)
## S4 method for signature 'gtypes'
getStrata(x)
setStrata(x) <- value
## S4 replacement method for signature 'gtypes'
setStrata(x) <- value
getSchemes(x, ...)
## S4 method for signature 'gtypes'
getSchemes(x, ...)
setSchemes(x) <- value
## S4 replacement method for signature 'gtypes'
setSchemes(x) <- value
getSequences(x, ...)
## S4 method for signature 'gtypes'
getSequences(x, as.haplotypes = TRUE, seqName = NULL, as.multidna = FALSE, ...)
getDescription(x, ...)
## S4 method for signature 'gtypes'
getDescription(x, ...)
setDescription(x) <- value
## S4 replacement method for signature 'gtypes'
setDescription(x) <- value
getOther(x, ...)
## S4 method for signature 'gtypes'
getOther(x, value = NULL, ...)
setOther(x, name) <- value
## S4 replacement method for signature 'gtypes'
setOther(x, name) <- value
## S4 method for signature 'gtypes,ANY,ANY,ANY'
x[i, j, k, ..., quiet = TRUE, drop = FALSE]
|
x |
a gtypes object. |
by.strata |
logical - return results by strata? |
... |
other arguments passed from generics (ignored). |
value |
value being assigned by accessor. |
as.haplotypes |
return sequences as haplotypes? If |
seqName |
the name (or number) of a set of sequences from the
|
as.multidna |
return sequences as a multidna object? If
|
name |
name of the value going into the |
i, j, k |
subsetting slots for individuals ( |
quiet |
suppress warnings about unmatched requested individuals, loci, or strata? |
drop |
if |
Indexing a gtypes
object with integers, characters, or
logicals with the [
operator follows the same rules as normal indexing
in R. The order that individuals, loci, and strata are chosen is the order
returned by getIndNames
, getLocNames
, and getStrataNames
respectively. If unstratified samples are present, they can be selected as a
group either by including NA
in the character or numeric vector of the
k
slot, or by providing a logical vector based on
is.na(strata(g))
to the i
slot.
number of individuals
number of loci
number of strata
vector of individual/sample names
vector of locus names
vector of strata names for current scheme
number of alleles at each locus
contents of
@other
slot
return or modify the current stratification
return or modify the current stratification schemes
return a list of alleles at each locus
return the multidna object in the
@sequences
slot. See getSequences
to extract
individual genes or sequences from this object
return the object's description
Eric Archer eric.archer@noaa.gov
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | #--- create a diploid (microsatellite) gtypes object
data(msats.g)
msats.g <- stratify(msats.g, "fine")
getNumStrata(msats.g)
getStrataNames(msats.g)
getNumLoci(msats.g)
getLociNames(msats.g)
# reassign all samples to two randomly chosen strata
new.strata <- sample(c("A", "B"), getNumInd(msats.g), rep = TRUE)
names(new.strata) <- getIndNames(msats.g)
setStrata(msats.g) <- new.strata
msats.g
#--- a sequence example
library(ape)
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
wood.g <- sequence2gtypes(x)
new.strata <- sample(c("A", "B"), getNumInd(wood.g), rep = TRUE)
names(new.strata) <- getIndNames(wood.g)
setStrata(wood.g) <- new.strata
wood.g
# get the multidna sequence object
multi.seqs <- getSequences(wood.g, as.multidna = TRUE)
class(multi.seqs) # "multidna"
# get a list of DNAbin objects
dnabin.list <- getSequences(wood.g)
class(dnabin.list) # "list"
# get a DNAbin object of the first locus
dnabin.1 <- getSequences(wood.g)[[1]]
class(dnabin.1) # "DNAbin"
# getting and setting values in the `other` slot:
getOther(dloop.g)
setOther(dloop.g, "timestamp") <- timestamp()
setOther(dloop.g, "Author") <- "Hoban Washburne"
getOther(dloop.g)
getOther(dloop.g, "timestamp")
setOther(dloop.g, "Author") <- NULL
getOther(dloop.g)
|
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