Extract the from the 1KG GDS 'sample.ref' node for the reference profiles (real ancestry assignation)

Source: R/process1KG.R

The function extract the specified column for the 'sample.ref' node present in the Reference GDS file. The column must be present in the data.frame saved in the 'sample.ref' node. Only the information for the reference profiles is returned. The values represent the known ancestry assignation.

getRefSuperPop(fileReferenceGDS)

Arguments

fileReferenceGDS

a character string representing the file name of the Reference GDS file. The file must exist.

Value

vector of character strings representing the content of the extracted column for the 1KG GDS 'sample.ref' node. The values represent the known ancestry assignation. The profile identifiers are used as names for the vector.

Author

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples



## Path to the demo pedigree file is located in this package
dataDir <- system.file("extdata", package="RAIDS")

## Open existing demo 1K GDS file with "sample.ref" node
nameFileGDS <- file.path(dataDir, "PopulationReferenceDemo.gds")

## Extract super population information for the 1KG profiles
getRefSuperPop(fileReferenceGDS=nameFileGDS)
#> HG00100 HG00101 HG00102 HG00103 HG00104 HG00105 HG00106 HG00109 
#>   "EUR"   "SAS"   "EAS"   "EUR"   "AFR"   "AFR"   "AFR"   "AMR"