convertNcdfGds: Convert between NetCDF and GDS format

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

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)

smgogarten/GWASTools documentation built on May 18, 2024, 1:19 a.m.