Combines two genlight objects — gl.join • dartR

This function combines two genlight objects and their associated metadata. The history associated with the two genlight objects is cleared from the new genlight object. The individuals/samples must be the same in each genlight object.

The function is typically used to combine datasets from the same service where the files have been split because of size limitations. The data is read in from multiple csv files, then the resultant genlight objects are combined.

Usage

gl.join(x1, x2, verbose = NULL)

Arguments

x1: Name of the first genlight object [required].
x2: Name of the first genlight object [required].
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 specified using gl.set.verbosity].

Value

A new genlight object

Author

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

x1 <- testset.gl[,1:100]
x1@other$loc.metrics <-  testset.gl@other$loc.metrics[1:100,]
nLoc(x1)
#> [1] 100
x2 <- testset.gl[,101:150]
x2@other$loc.metrics <-  testset.gl@other$loc.metrics[101:150,]
nLoc(x2)
#> [1] 50
gl <- gl.join(x1, x2, verbose=2)
#> Starting gl.join 
#>   Concatenating two genlight objects, x1 and x2 
#>   Concatenating the locus metrics
#>   Adding the individual metrics
#>   Adding the latlons if they exist
#>   Setting the locus metrics flags
#>   Adding the history
#> Completed: gl.join 
#> 
nLoc(gl)
#> [1] 150