readGenalexExcel: Read GenAlEx-format genotypes from an Excel worksheet
In douglasgscofield/readGenalex: Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files

Description Usage Arguments Details Value Author(s) References See Also Examples

Reads genotype data file in GenAlEx format from an Excel worksheet into an annotated data frame of class genalex. Both .xls and .xlsx formats may be read. The same consistency checks are performed as for readGenalex. This function uses the function readWorksheetFromFile from the XLConnect package to read the Excel file. Strings representing NA values are strictly those allowed by GenAlEx itself, 0 and -1.

1	readGenalexExcel(file, worksheet, ploidy = 2)

`file`	Excel workbook file from which to read the worksheet
`worksheet`	Worksheet specification in a format accepted by `readWorksheetFromFile`, specifically the worksheet name, as a character string, or an integer value indicating the worksheet position in the workbook, e.g., 1, 2, etc.
`ploidy`	The ploidy of genotypes encoded in `worksheet` (defaults to 2)

This function is provided as a convenience to the user. If there are incompatibilities when reading GenAlEx-format data with this function, it is recommended to export the worksheet from Excel as tab-delimited text and read it with readGenalex.

An annotated data frame of class genalex. The format is described in more detail in readGenalex. The "data.file.name" attribute is set to the value "file(worksheet)".

Douglas G. Scofield

Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539.

Peakall, R. and Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295.

readGenalex, readWorksheetFromFile

## Not run: 
xl.file <- system.file("extdata/Qagr_genotypes.xlsx",
                       package = "readGenalex")
## this could take ~5 sec or longer
gt <- readGenalexExcel(xl.file, worksheet = "Qagr_pericarp_genotypes")
head(gt)
names(attributes(gt))

## End(Not run)