Imports DArT data into dartR and converts it into a genlight object
Source:R/gl.read.dart.r
gl.read.dart.RdThis function is a wrapper function that allows you to convert your DArT file into a genlight object in one step. In previous versions you had to use read.dart and then dart2genlight. In case you have individual metadata for each individual/sample you can specify as before in the dart2genlight command the file that combines the data.
Usage
gl.read.dart(
filename,
ind.metafile = NULL,
recalc = TRUE,
mono.rm = FALSE,
nas = "-",
topskip = NULL,
lastmetric = "RepAvg",
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
Force the recalculation of locus metrics, in case individuals have been manually deleted from the input csv file [default TRUE].
- mono.rm
Force the removal of monomorphic loci (including all NAs), in case individuals have been manually deleted from the input csv file [default FALSE].
- nas
A character specifying NAs [default '-'].
- topskip
A number specifying the number of rows to be skipped. If not provided the number of rows to be skipped are 'guessed' by the number of rows with '*' at the beginning [default NULL].
- lastmetric
Specifies the last non-genetic column (Default is 'RepAvg'). Be sure to check if that is true, otherwise the number of individuals will not match. You can also specify the last column by a number [default 'RepAvg'].
- covfilename
Use ind.metafile parameter [depreciated, NULL].
- service_row
The row number in which the information of the DArT service is contained [default 1].
- plate_row
The row number in which the information of the plate location is contained [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()].
Value
A genlight object that contains individual metrics [if data were provided] and locus metrics [from a DArT report].
Details
The dartR genlight object can then be fed into a number of initial screening,
export and export functions provided by the package. For some of the
functions it is necessary to have the metadata that was provided from DArT.
Please check the vignette for more information. Additional information can
also be found in the help documents for utils.read.dart.
Author
Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)
Examples
dartfile <- system.file('extdata','testset_SNPs_2Row.csv', package='dartR')
metadata <- system.file('extdata','testset_metadata.csv', package='dartR')
gl <- gl.read.dart(dartfile, ind.metafile = metadata, probar=TRUE)
#> Starting gl.read.dart
#> Starting utils.read.dart
#> Topskip not provided.
#> Setting topskip to 3 .
#> Reading in the SNP data
#> Detected 2 row format.
#> Number of rows per clone (should be only 2 s): 2
#> Added the following locus metrics:
#> AlleleID CloneID AlleleSequence SNP SnpPosition CallRate OneRatioRef OneRatioSnp TrimmedSequence FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RepAvg .
#> Recognised: 250 individuals and 255 SNPs in a 2 row format using /home/runner/work/_temp/Library/dartR/extdata/testset_SNPs_2Row.csv
#> Completed: utils.read.dart
#> Starting utils.dart2genlight
#> Starting conversion....
#> Format is 2 rows.
#> Please note conversion of bigger data sets will take some time!
#> Once finished, we recommend to save the object using save(object, file="object.rdata")
#>
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#> Adding individual metrics: /home/runner/work/_temp/Library/dartR/extdata/testset_metadata.csv .
#> Ids for individual metadata (at least a subset of) are matching!
#> Found 250 matching ids out of 250 ids provided in the ind.metadata file.
#> Added population assignments.
#> Added latlon data.
#> Added id to the other$ind.metrics slot.
#> Added pop to the other$ind.metrics slot.
#> Added lat to the other$ind.metrics slot.
#> Added lon to the other$ind.metrics slot.
#> Added sex to the other$ind.metrics slot.
#> Added maturity to the other$ind.metrics slot.
#> Completed: utils.dart2genlight
#> Data read in. Please check carefully the output above
#> Read depth calculated and added to the locus metrics
#> Minor Allele Frequency (MAF) calculated and added to the locus metrics
#> Recalculating locus metrics provided by DArT (optionally specified)
#> Completed: gl.read.dart
#>