convertNcdfGds {GWASTools} | R Documentation

## Convert between NetCDF and GDS format

### Description

`convertNcdfGds` converts a NetCDF file to GDS format.

`convertGdsNcdf` converts a GDS file to NetCDF format.

`checkNcdfGds` checks whether a genotype NetCDF file and a GDS file contain identical data.

### Usage

    convertNcdfGds(ncdf.filename, gds.filename, snp.annot = NULL,
      precision = "single", compress = "LZMA_RA", verbose = TRUE)

    convertGdsNcdf(gds.filename, ncdf.filename,
      precision = "single", verbose = TRUE)

    checkNcdfGds(ncdf.filename, gds.filename, verbose = TRUE)

### Arguments

`ncdf.filename` | name of the NetCDF file
`gds.filename` | name of the GDS file
`snp.annot` | a `SnpAnnotationDataFrame` with SNP annotation. The column named "snpName" will be written to "snp.rs.id" in the GDS file.
`precision` | A character value indicating whether floating point numbers should be stored as "double" or "single" precision.
`compress` | The compression level for variables in a GDS file (see `add.gdsn` for options.
`verbose` | whether to show progress information

### Details

`convertNcdfGds` assumes any variables other than "sampleID", "chromosome", and "position" have dimensions SNP x sample.

If `snp.annot` has columns "rsID", "alleleA", "alleleB", these will be stored in the GDS file as "snp.rs.id" and "snp.allele" (the latter has the format "A/B").

Chromosome codes from `snp.annot` (for autosomes, X, Y, etc.) will be stored in the GDS file.

`convertGdsNcdf` assumes any variables not starting with "snp" or "sample" have dimensions SNP x sample.

### Value

`checkNcdfGds` returns `TRUE` if the NetCDF and GDS files contain identical data. If the files differ, it will print a diagnostic message and return `FALSE`.

### Author(s)

Xiuwen Zheng, Stephanie Gogarten

### See Also

gdsfmt, ncdf4-package

### Examples

    library(GWASdata)
    ncfile <- system.file("extdata", "illumina_geno.nc", package="GWASdata")

    data(illuminaSnpADF)

    gdsfile <- tempfile()
    convertNcdfGds(ncfile, gdsfile, snp.annot=illuminaSnpADF)

    checkNcdfGds(ncfile, gdsfile)

    ncfile2 <- tempfile()
    convertGdsNcdf(gdsfile, ncfile2)

    file.remove(gdsfile, ncfile2)

[Package GWASTools version 1.33.3 Index]