Read an FSTAT file into a tidy or wide data frame

Used internally in genometranslator and might be of interest for users. The function read_fstat reads a file in the fstat file (Goudet, 1995) into a wide or long/tidy data frame

To manipulate and prune the dataset prior to tidying, use the functions tidy_genome and genome_translator, that uses blacklist and whitelist along several other filtering options.

Usage

read_fstat(data, strata = NULL, tidy = TRUE, filename = NULL, verbose = FALSE)

Arguments

data: A fstat filename with extension .dat.
strata: (optional) A tab delimited file with 2 columns. Header: INDIVIDUALS and STRATA. The STRATA column can be any hierarchical grouping. To create a strata file see individuals2strata. Default: strata = NULL.
tidy: (optional, logical) With tidy = FALSE, the markers are the variables and the genotypes the observations (wide format). With the default: tidy = TRUE, markers and genotypes are variables with their own columns (long format). Default: tidy = TRUE.
filename: (optional) The file name for the tidy data frame written to the working directory. With the default, The tidy data is in the global environment only (i.e. not written in the working directory). Default: filename = NULL.
verbose: Logical indicating whether progress messages are emitted. Default: verbose = FALSE.

Value

The output in your global environment is a wide or long/tidy data frame. If filename is provided, the wide or long/tidy data frame is also written to the working directory.

Dependencies

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

References

Goudet J. (1995). FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity 86:485-486

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
# We will use the fstat dataset provided with adegenet package
require("hierfstat")

# The simplest form of the function:
fstat.file <- genometranslator::read_fstat(
    data = system.file(
    "extdata/diploid.dat",
    package = "hierfstat"
    )
 )

# To output a data frame in wide format, with markers in separate columns:
nancycats.wide <- genometranslator::read_fstat(
    data = system.file(
        "extdata/diploid.dat",
        package = "hierfstat"
    ),
tidy = FALSE
)
} # }