gl.read.dart {dartR.base}

Imports DArT data into dartR and converts it into a dartR genlight object

Description

This function is a wrapper function that allows you to convert your DArT file into a genlight object of class dartR.

Usage

gl.read.dart(
  filename,
  ind.metafile = NULL,
  recalc = TRUE,
  mono.rm = FALSE,
  nas = "-",
  topskip = NULL,
  lastmetric = NULL,
  covfilename = NULL,
  service.row = 1,
  plate.row = 3,
  probar = FALSE,
  verbose = NULL
)

Arguments

filename

File containing the SNP data (csv file) [required].

ind.metafile

File that contains additional information on individuals [required].

recalc

If TRUE, force the recalculation of locus metrics [default TRUE].

mono.rm

If TRUE, force the removal of monomorphic loci (including all NAs. [default FALSE].

nas

A character specifying NAs [default '-'].

topskip

A number specifying the number of initial rows to be skipped [default NULL].

lastmetric

Deprecated, specifies the last column of locus metadata. Can be specified as a column number [default NULL].

covfilename

Deprecated, sse ind.metafile parameter [NULL].

service.row

The row number for the DArT service is contained [default 1].

plate.row

The row number the plate well [default 3].

probar

Show progress bar [default FALSE].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2, or as set by gl.set.verbose()].

Details

The function will determine automatically if the data are in Diversity Arrays one-row csv format or two-row csv format. The first row of data is determined from the number of rows with an * in the first column. This can be alternatively specified with the topskip parameter. The DArT service code is added to the ind.metrics of the genlight object. The row containing the service code for each individual can be specified with the service.row parameter. #'The DArT plate well is added to the ind.metrics of the genlight object. The row containing the plate well for each individual can be specified with the plate.row parameter. If individuals have been deleted from the input file manually, then the locus metrics supplied by DArT will no longer be correct and some loci may be monomorphic. To accommodate this, set mono.rm and recalc to TRUE.

Value

A dartR genlight object that contains individual and locus metrics [if data were provided] and locus metrics [from a DArT report].

Author(s)

Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

See Also

utils.read.dart

Other io: gl.load(), gl.read.csv(), gl.read.fasta(), gl.read.silicodart(), gl.read.vcf(), gl.save(), gl.write.csv(), utils.read.dart()

Examples

dartfile <- system.file('extdata','testset_SNPs_2Row.csv', package='dartR.data')
metadata <- system.file('extdata','testset_metadata.csv', package='dartR.data')
gl <- gl.read.dart(dartfile, ind.metafile = metadata, probar=TRUE)