GWASTools (version 1.12.2)

ncdfSubset: Write a subset of data in a netCDF file to a new netCDF file

Description

ncdfSubset takes a subset of data (snps and samples) from a netCDF file and write it to a new netCDF file. ncdfSubsetCheck checks that a netCDF file is the desired subset of another netCDF file.

Usage

ncdfSubset(parent.ncdf, sub.ncdf, sample.include=NULL, snp.include=NULL, verbose=TRUE)
ncdfSubsetCheck(parent.ncdf, sub.ncdf, sample.include=NULL, snp.include=NULL, verbose=TRUE)

Arguments

parent.ncdf

Name of the parent netCDF file

sub.ncdf

Name of the subset netCDF file

sample.include

Vector of sampleIDs to include in sub.ncdf

snp.include

Vector of snpIDs to include in sub.ncdf

verbose

Logical value specifying whether to show progress information.

Details

ncdfSubset can select a subset of snps for all samples by setting snp.include, a subset of samples for all snps by setting sample.include, or a subset of snps and samples with both arguments.

See Also

ncdf, createDataFile

Examples

ncfile <- system.file("extdata", "affy_geno.nc", package="GWASdata")
nc <- NcdfGenotypeReader(ncfile)
sample.sel <- getScanID(nc, index=1:10)
snp.sel <- getSnpID(nc, index=1:100)
close(nc)

subnc <- tempfile()
ncdfSubset(ncfile, subnc, sample.include=sample.sel, snp.include=snp.sel)
ncdfSubsetCheck(ncfile, subnc, sample.include=sample.sel, snp.include=snp.sel)
file.remove(subnc)