NcdfReader {GWASTools}R Documentation

Class NcdfReader

Description

The NcdfReader class is a wrapper for the ncdf4-package that provides an interface for reading NetCDF files.

Constructor

NcdfReader(filename):

filename must be the path to a NetCDF file.

The NcdfReader constructor creates and returns a NcdfReader instance pointing to this file.

Accessors

In the code snippets below, object is a NcdfReader object.

getVariable(object, varname, start, count, drop=TRUE): Returns the contents of the variable varname.

The result is a vector, matrix, or array, depending on the number of dimensions in the returned values and the value of drop. Missing values (specified by a "missing_value" attribute, see ncvar_change_missval) are represented as NA. If the variable is not found in the NetCDF file, returns NULL.

getVariableNames(object): Returns names of variables in the NetCDF file.

getDimension(object, varname): Returns dimension for NetCDF variable varname.

getDimensionNames(object, varname): Returns names of dimensions in the NetCDF file. If varname is provided, returns dimension names for NetCDF variable varname.

getAttribute(object, attname, varname): Returns the attribute attname associated with the variable varname. If varname is not specified, attname is assumed to be a global attribute.

hasCoordVariable(object, varname): Returns TRUE if varname is a coordinate variable (a variable with the same name as a dimension).

hasVariable(object, varname): Returns TRUE if varname is a variable in the NetCDF file (including coordinate variables).

Standard Generic Methods

In the code snippets below, object is a NcdfReader object.

open(object): Opens a connection to a NetCDF file.

close(object): Closes the connection to a NetCDF file.

show(object): Summarizes the contents of a NetCDF file.

Author(s)

Stephanie Gogarten

See Also

ncdf4-package, NcdfGenotypeReader, NcdfIntensityReader

Examples

file <- system.file("extdata", "affy_geno.nc", package="GWASdata")
nc <- NcdfReader(file)

getDimensionNames(nc)
getVariableNames(nc)

hasVariable(nc, "genotype")
geno <- getVariable(nc, "genotype", start=c(1,1), count=c(10,10))

close(nc)

[Package GWASTools version 1.36.0 Index]