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Export data from genind objects to genalex formatted \*.csv files.

Source: R/file_handling.r
genind2genalex.Rd

genind2genalex will export a genclone or genind object to a \*.csv file formatted for use in genalex.

Usage

genind2genalex(
  gid,
  filename = "",
  overwrite = FALSE,
  quiet = FALSE,
  pop = NULL,
  allstrata = TRUE,
  geo = FALSE,
  geodf = "xy",
  sep = ",",
  sequence = FALSE
)

Arguments

gid

a genclone or genind object.

filename

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()

overwrite

logical if FALSE (default) and filename exists, then the file will not be overwritten. Set this option to TRUE to overwrite the file.

quiet

logical If FALSE a message will be printed to the screen.

pop

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.

allstrata

if this is TRUE, the strata will be combined into a single population factor in the genalex file.

geo

logical Default is FALSE. If it is set to TRUE, the resulting file will have two columns for geographic data.

geodf

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".

sep

a character specifying what character to use to separate columns. Defaults to ",".

sequence

when TRUE, sequence data will be converted to integers as per the GenAlEx specifications.

Value

The the file path or connection where the data were written.

Note

If your data set lacks a population structure, it will be coded in the new file as a single population labeled "Pop". Likewise, if you don't have any labels for your individuals, they will be labeled as "ind1" through "indN", with N being the size of your population.

See also

read.genalex(), clonecorrect(), genclone, genind

Author

Zhian N. Kamvar

Examples

# \dontrun{
data(nancycats)
genind2genalex(nancycats, "~/Documents/nancycats.csv", geo=TRUE)
#> Extracting the table ... Writing the table to ~/Documents/nancycats.csv ... Done.
#> [1] "~/Documents/nancycats.csv"
# }