GWASTools (version 1.12.2)

ncdfCreate: Write genotypic calls and/or associated metrics to a netCDF file - deprecated

Description

Deprecated - use createDataFile

The function creates a shell netCDF file to which data can subsequently written.

Usage

ncdfCreate(snp.annotation, ncdf.filename, variables = "genotype",  n.samples = 10, precision = "double", array.name = NULL, genome.build = NULL)

Arguments

snp.annotation

Snp annotation dataframe with columns "snpID", "chromosome", and "position". snpID should be a unique integer vector, sorted with respect to chromosome and position.

ncdf.filename

The name of the genotype netCDF file to create

variables

A character vector containing the names of the variables to create (must be one or more of c("genotype", "quality", "X", "Y", "rawX", "rawY", "R", "Theta", "BAlleleFreq", "LogRRatio"))

n.samples

The number of samples that will be in the netcdf file.

precision

A character value indicating whether floating point numbers should be stored as "double" or "single" precision.

array.name

Name of the array, to be stored as an attribute in the netCDF file.

genome.build

Genome build used in determining chromosome and position, to be stored as an attribute in the netCDF file.

Details

The function creates a shell netCDF file to which data can subsequently written.

See Also

ncdf, ncdfAddData, ncdfSubset

Examples

## Not run: 
# library(GWASdata)
# data(affy_snp_annot)
# ncfile <- tempfile()
# ncdfCreate(affy_snp_annot, ncfile, variables="genotype", n.samples=5)
# file.remove(ncfile)
# ## End(Not run)