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Defines a new population in a genlight object for specified individuals

Source: R/gl.define.pop.r
gl.define.pop.Rd

The script reassigns existing individuals to a new population and removes their existing population assignment.

The script returns a genlight object with the new population assignment.

Usage

gl.define.pop(x, ind.list, new, verbose = NULL)

Arguments

x

Name of the genlight object containing SNP genotypes [required].

ind.list

A list of individuals to be assigned to the new population [required].

new

Name of the new population [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 genlight object with the redefined population structure.

Author

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

Examples

popNames(testset.gl)
#>  [1] "EmmacBrisWive"    "EmmacBurdMist"    "EmmacBurnBara"    "EmmacClarJack"   
#>  [5] "EmmacClarYate"    "EmmacCoopAvin"    "EmmacCoopCully"   "EmmacCoopEulb"   
#>  [9] "EmmacFitzAllig"   "EmmacJohnWari"    "EmmacMaclGeor"    "EmmacMaryBoru"   
#> [13] "EmmacMaryPetr"    "EmmacMDBBowm"     "EmmacMDBCond"     "EmmacMDBCudg"    
#> [17] "EmmacMDBForb"     "EmmacMDBGwyd"     "EmmacMDBMaci"     "EmmacMDBMurrMung"
#> [21] "EmmacMDBSanf"     "EmmacNormJack"    "EmmacNormLeic"    "EmmacNormSalt"   
#> [25] "EmmacRichCasi"    "EmmacRoss"        "EmmacRussEube"    "EmmacTweeUki"    
#> [29] "EmsubRopeMata"    "EmvicVictJasp"   
gl <- gl.define.pop(testset.gl, ind.list=c('AA019073','AA004859'), 
new='newguys')
#> Starting gl.define.pop 
#>   Processing genlight object with SNP data
#>   Warning: genlight object contains monomorphic loci
#>   Assigned listed individuals AA019073, AA004859 to new population newguys 
#> Completed: gl.define.pop 
#> 
popNames(gl)
#>  [1] "EmmacBrisWive"    "EmmacBurdMist"    "EmmacBurnBara"    "EmmacClarJack"   
#>  [5] "EmmacClarYate"    "EmmacCoopAvin"    "EmmacCoopCully"   "EmmacCoopEulb"   
#>  [9] "EmmacFitzAllig"   "EmmacJohnWari"    "EmmacMDBBowm"     "EmmacMDBCond"    
#> [13] "EmmacMDBCudg"     "EmmacMDBForb"     "EmmacMDBGwyd"     "EmmacMDBMaci"    
#> [17] "EmmacMDBMurrMung" "EmmacMDBSanf"     "EmmacMaclGeor"    "EmmacMaryBoru"   
#> [21] "EmmacMaryPetr"    "EmmacNormJack"    "EmmacNormLeic"    "EmmacNormSalt"   
#> [25] "EmmacRichCasi"    "EmmacRoss"        "EmmacRussEube"    "EmmacTweeUki"    
#> [29] "EmsubRopeMata"    "EmvicVictJasp"    "newguys"         
indNames(gl)[pop(gl)=='newguys']
#> [1] "AA019073" "AA004859"