NcdfReader-class: Class NcdfReader
In GWASTools: Tools for Genome Wide Association Studies

Description Constructor Accessors Standard Generic Methods Author(s) See Also Examples

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

NcdfReader(filename):

filename must be the path to a NetCDF file.

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

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

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

start is a vector of integers indicating where to start reading values. The length of this vector must equal the number of dimensions the variable has. If not specified, reading starts at the beginning of the file (1,1,...).
count is a vector of integers indicating the count of values to read along each dimension. The length of this vector must equal the number of dimensions the variable has. If not specified and the variable does NOT have an unlimited dimension, the entire variable is read. As a special case, the value "-1" indicates that all entries along that dimension should be read.
drop is a logical for whether the result will be coerced to the lowest possible dimension.

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).

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.

Stephanie Gogarten

ncdf4-package, NcdfGenotypeReader, NcdfIntensityReader

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)