The PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA.

Source: R/RAIDS.R

The object is a list.

data(demoPCASyntheticProfiles)

Format

The list containing the PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA. The list contains 3 entries:

sample.id

a character string representing the unique identifier of the synthetic profiles.

eigenvector.ref

a matrix of numeric containing the eigenvectors for the reference profiles.

eigenvector

a matrix of numeric containing the eigenvectors for the current synthetic profiles projected on the demo PCA 1KG reference profiles.

Value

The list containing the PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA. The list contains 3 entries:

sample.id

a character string representing the unique identifier of the synthetic profiles.

eigenvector.ref

a matrix of numeric containing the eigenvectors for the reference profiles.

eigenvector

a matrix of numeric containing the eigenvectors for the current synthetic profiles projected on the demo PCA 1KG reference profiles.

Details

This object can be used to test the computeKNNRefSynthetic function.

See also

computeKNNRefSynthetic

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

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      EAS
#> 2 1.ex1.HG00246.1 2 3      AMR
#> 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)