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
1 2 3 4 5 6 7 8 9 10 | 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)
|
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