The pedigree information about a demo profile called 'ex1'.

The object is a data.frame.

data(demoPedigreeEx1)

Format

The data.frame containing the information about a demo profile called 'ex1'. the data.frame has 5 columns:

Name.ID

a character string representing the unique identifier of the profile.

Case.ID

a character string representing the unique identifier of the case associated to the profile.

Sample.Type

a character string describing the type of profile.

Diagnosis

a character string describing the diagnosis of the profile.

Source

a character string describing the source of the profile.

Value

The data.frame containing the information about a demo profile called 'ex1'. the data.frame has 5 columns:

Name.ID

a character string representing the unique identifier of the profile.

Case.ID

a character string representing the unique identifier of the case associated to the profile.

Sample.Type

a character string describing the type of profile.

Diagnosis

a character string describing the diagnosis of the profile.

Source

a character string describing the source of the profile.

Details

This object can be used to test the runExomeAncestry function.

See also

runExomeAncestry

for running runs most steps leading to the ancestry inference call on a specific exome profile.

Examples

## Required library for GDS
library(SNPRelate)

## Path to the demo 1KG GDS file is located in this package
dataDir <- system.file("extdata", package="RAIDS")

#################################################################
## Load the information about the profile
#################################################################
data(demoPedigreeEx1)
head(demoPedigreeEx1)
#>     Name.ID Case.ID   Sample.Type Diagnosis     Source
#> ex1     ex1     ex1 Primary Tumor    Cancer Databank B

#################################################################
## The 1KG GDS file and the 1KG SNV Annotation GDS file
## need to be located in the same directory
## Note that the 1KG GDS file used for this example is a
## simplified version and CANNOT be used for any real analysis
#################################################################
path1KG <- file.path(dataDir, "tests")

fileReferenceGDS  <- file.path(path1KG, "ex1_good_small_1KG.gds")
fileAnnotGDS <- file.path(path1KG, "ex1_good_small_1KG_Annot.gds")

#################################################################
## The Sample SNP pileup files (one per sample) need
## to be located in the same directory.
#################################################################
pathGeno <- file.path(dataDir, "example", "snpPileup")

#################################################################
## The path where the Profile GDS Files (one per sample)
## will be created need to be specified.
#################################################################
pathProfileGDS <- file.path(tempdir(), "out.tmp")

pathOut <- file.path(tempdir(), "res.out")

#################################################################
## A data frame containing general information about the study
## is also required. The data frame must have
## those 3 columns: "studyID", "study.desc", "study.platform"
#################################################################
studyDF <- data.frame(study.id="MYDATA",
                        study.desc="Description",
                        study.platform="PLATFORM",
                        stringsAsFactors=FALSE)

####################################################################
## Fix seed to ensure reproducible results
####################################################################
set.seed(2043)

gds1KG <- snpgdsOpen(fileReferenceGDS)
dataRef <- select1KGPop(gds1KG, nbProfiles=2L)
closefn.gds(gds1KG)

## Required library for this example to run correctly
if (requireNamespace("GenomeInfoDb", quietly=TRUE) &&
     requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly=TRUE)) {

    ## Chromosome length information
    ## chr23 is chrX, chr24 is chrY and chrM is 25
    chrInfo <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg38::Hsapiens)[1:25]

    # \donttest{
        runExomeAncestry(pedStudy=demoPedigreeEx1, studyDF=studyDF,
            pathProfileGDS=pathProfileGDS,
            pathGeno=pathGeno, pathOut=pathOut,
            fileReferenceGDS=fileReferenceGDS,
            fileReferenceAnnotGDS=fileAnnotGDS,
            chrInfo=chrInfo, syntheticRefDF=dataRef,
            genoSource="snp-pileup")

        unlink(pathProfileGDS, recursive=TRUE, force=TRUE)
        unlink(pathOut, recursive=TRUE, force=TRUE)
    # }
}