Append information associated to blocks, as indexes, into the Population Reference SNV Annotation GDS file

The function appends the information about the blocks into the Population Reference SNV Annotation GDS file. The information is extracted from the Population Reference GDS file.

addGeneBlockGDSRefAnnot(
  gdsReference,
  gdsRefAnnotFile,
  winSize = 10000,
  ensDb,
  suffixBlockName
)

Arguments

gdsReference

an object of class gds.class (a GDS file), the opened Reference GDS file.

gdsRefAnnotFile

a character string representing the file name corresponding the Reference SNV Annotation GDS file. The function will open it in write mode and close it after. The file must exist.

winSize

a single positive integer representing the size of the window to use to group the SNVs when the SNVs are in a non-coding region. Default: 10000L.

ensDb

An object with the ensembl genome annotation Default: EnsDb.Hsapiens.v86.

suffixBlockName

a character string that identify the source of the block and that will be added to the block description into the Reference SNV Annotation GDS file, as example: Ensembl.Hsapiens.v86.

Value

The integer OL when the function is successful.

Author

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Required library
library(SNPRelate)

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

fileAnnotGDS <- file.path(tempdir(), "ex1_good_small_1KG_Ann_GDS.gds")

## Required library
if (requireNamespace("EnsDb.Hsapiens.v86", quietly=TRUE)) {

    file.copy(file.path(dataDir, "tests",
        "ex1_NoBlockGene.1KG_Annot_GDS.gds"), fileAnnotGDS)

    ## Making a "short cut" on the ensDb object
    edb <- EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86

    ## GDS Reference file
    fileReferenceGDS  <- file.path(dataDir, "tests",
                "ex1_good_small_1KG.gds")

    # \donttest{
        ## Open the reference GDS file (demo version)
        gds1KG <- snpgdsOpen(fileReferenceGDS)

        ## Append information associated to blocks
        addGeneBlockGDSRefAnnot(gdsReference=gds1KG,
            gdsRefAnnotFile=fileAnnotGDS,
            ensDb=edb,
            suffixBlockName="EnsDb.Hsapiens.v86")

        gdsAnnot1KG <- openfn.gds(fileAnnotGDS)
        print(gdsAnnot1KG)
        print(read.gdsn(index.gdsn(gdsAnnot1KG, "block.annot")))

       ## Close GDS files
       closefn.gds(gds1KG)
       closefn.gds(gdsAnnot1KG)
    # }

    ## Remove temporary file
    unlink(fileAnnotGDS, force=TRUE)

}
#> File: /tmp/RtmpONDtC4/ex1_good_small_1KG_Ann_GDS.gds (392.5K)
#> +    [  ]
#> |--+ phase   { Bit2 11000x156 LZ4_ra(21.5%), 90.2K }
#> |--+ block.annot   [ data.frame ] *
#> |  |--+ block.id   { Str8 7, 119B }
#> |  \--+ block.desc   { Str8 7, 384B }
#> \--+ block   { Int32 11000x7 LZ4_ra(22.5%), 67.6K }
#>                   block.id
#> 1            EAS.0.05.500k
#> 2            EUR.0.05.500k
#> 3            AFR.0.05.500k
#> 4            AMR.0.05.500k
#> 5            SAS.0.05.500k
#> 6  Gene.EnsDb.Hsapiens.v86
#> 7 GeneS.EnsDb.Hsapiens.v86
#>                                                      block.desc
#> 1         EAS populationblock base on SNP 0.05 and windows 500k
#> 2         EUR populationblock base on SNP 0.05 and windows 500k
#> 3         AFR populationblock base on SNP 0.05 and windows 500k
#> 4         AMR populationblock base on SNP 0.05 and windows 500k
#> 5         SAS populationblock base on SNP 0.05 and windows 500k
#> 6 List of blocks including overlapping genes EnsDb.Hsapiens.v86
#> 7           List of blocks of split by genes EnsDb.Hsapiens.v86