The known super population ancestry of the demo 1KG reference profiles.

Source: R/RAIDS.R

The object is a vector.

data(demoKnownSuperPop1KG)

Format

The vector containing the know super population ancestry for the demo 1KG reference profiles.

Value

The vector containing the know super population ancestry for the demo 1KG reference profiles.

Details

This object can be used to test the computeKNNRefSynthetic and computePoolSyntheticAncestryGr functions.

See also

computeKNNRefSynthetic

for running a k-nearest neighbors analysis on a subset of the synthetic data set.

computePoolSyntheticAncestryGr

for running a PCA analysis using 1 synthetic profile from each sub-continental population.

Examples


## Required library
library(gdsfmt)

## Load the demo PCA on the synthetic profiles projected on the
## demo 1KG reference PCA
data(demoPCASyntheticProfiles)

## Load the known ancestry for the demo 1KG reference profiles
data(demoKnownSuperPop1KG)

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

## Open the Profile GDS file
gdsProfile <- snpgdsOpen(file.path(dataDir, "ex1.gds"))

# The name of the synthetic study
studyID <- "MYDATA.Synthetic"

## Projects synthetic profiles on 1KG PCA
results <- computeKNNRefSynthetic(gdsProfile=gdsProfile,
    listEigenvector=demoPCASyntheticProfiles,
    listCatPop=c("EAS", "EUR", "AFR", "AMR", "SAS"), studyIDSyn=studyID,
    spRef=demoKnownSuperPop1KG)

## The inferred ancestry for the synthetic profiles for different values
## of D and K
head(results$matKNN)
#>         sample.id D K SuperPop
#> 1 1.ex1.HG00246.1 2 2      SAS
#> 2 1.ex1.HG00246.1 2 3      SAS
#> 3 1.ex1.HG00246.1 2 4      EAS
#> 4 1.ex1.HG00246.1 2 5      EUR
#> 5 1.ex1.HG00246.1 2 6      EUR
#> 6 1.ex1.HG00246.1 2 7      EAS

## Close Profile GDS file (important)
closefn.gds(gdsProfile)