as.loci {pegas} | R Documentation |
These functions do conversion among different allelic data classes.
as.loci(x, ...) ## S3 method for class 'genind': as.loci(x, ...) genind2loci(x) ## S3 method for class 'data.frame': as.loci(x, allele.sep = "/", col.pop = "none", col.loci = NULL, ...) loci2genind(x) ## S3 method for class 'factor': as.loci(x, allele.sep = "/", ...) ## S3 method for class 'character': as.loci(x, allele.sep = "/", ...)
x |
an object of class "loci" or "genind" , a data
frame, a factor, or a vector of mode character. |
allele.sep |
the character(s) separating the alleles for each locus in the data file (a forward slash by default). |
col.pop |
specifies whether one of the column of the data file
identifies the population; default "none" , otherwise an
integer giving the number of the column. |
col.loci |
a vector of integers specifying the indices of the columns that are loci. By default, all columns are taken as loci except the one labelled "population", if present. |
... |
further arguments to be passed to or from other methods. |
The main objectives of these functions is to provide easy conversion
between the data structures of adegenet and pegas, so both
packages can be used together smoothly. In addition, it is possible to
create a "loci"
object directly from a data frame, a vector, or
a factor.
genind2loci(x)
and as.loci(x)
are the same if x
is of class "genind"
.
An object of class c("loci", "data.frame")
for as.loci
and genind2loci
; an object of class "genind"
for
loci2genind
.
Emmanuel Paradis
read.loci
, genind
,
df2genind
for converting data frames to "genind"
x <- c("A-A", "A-a", "a-a") as.loci(x, allele.sep = "-") require(adegenet) data(nancycats) x <- as.loci(nancycats) y <- loci2genind(x) # back to "genind" identical(nancycats@tab, y@tab) identical(nancycats@pop, y@pop)