genind2genalex will export a genclone or genind object to a \*.csv file formatted for use in genalex.
genind2genalex(
gid,
filename = "",
overwrite = FALSE,
quiet = FALSE,
pop = NULL,
allstrata = TRUE,
geo = FALSE,
geodf = "xy",
sep = ",",
sequence = FALSE
)
The the file path or connection where the data were written.
a genclone or genind object.
a string indicating the name and/or path of the file you wish
to create. If this is left unchanged, the results will be saved in a
temporary file and a warning will be displayed for six seconds before the
file is written. This process should give you time to cancel the process
and choose a file path. Otherwise, the name of the file is returned, so you
can copy that to a file of your choice with file.copy()
logical
if FALSE
(default) and filename
exists, then
the file will not be overwritten. Set this option to TRUE
to overwrite
the file.
logical
If FALSE
a message will be printed to the
screen.
a character vector OR formula specifying the population factor.
This can be used to specify a specific subset of strata or custom
population factor for the output. Note that the allstrata
command
has precedence over this unless the value of this is a new population
factor.
if this is TRUE
, the strata will be combined into a
single population factor in the genalex file.
logical
Default is FALSE
. If it is set to
TRUE
, the resulting file will have two columns for geographic data.
character
Since the other
slot in the adegenet
object can contain many different items, you must specify the name of the
data frame in the other
slot containing your geographic coordinates.
It defaults to "xy".
a character specifying what character to use to separate columns. Defaults to ",".
when TRUE
, sequence data will be converted to integers
as per the GenAlEx specifications.
Zhian N. Kamvar
read.genalex()
, clonecorrect()
, genclone, genind
if (FALSE) {
data(nancycats)
genind2genalex(nancycats, "~/Documents/nancycats.csv", geo=TRUE)
}
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