DSArray: DSArray constructor

In PeteHaitch/DSArray: Compressed In-Memory Representation of 3-Dimensional Arrays That Contain Many Duplicate Slices

Description

Construct a DSArray from a 3-dimensional array, a matrix, or a list of matrix objects with identical dimensions.

Usage

DSArray(x, ...)

## S4 method for signature 'matrix'
DSArray(x, dimnames = NULL)

## S4 method for signature 'list'
DSArray(x, dimnames = NULL)

## S4 method for signature 'array'
DSArray(x, MARGIN = 2L, dimnames = NULL)

## S4 method for signature 'missing'
DSArray(x, ...)

Arguments

x	A 3-dimensional array, a list of matrix objects with identical dimensions, or a matrix.
...	Further arguments passed to other methods
dimnames	A dimnames attribute for the DSArray: NULL or a list of length 3. An empty list is treated as NULL, a list of length one as row names, and a list of length two as row names and column names. If NULL, the dimnames are constructed from x; see 'Dimnames' below.
MARGIN	An integer given the dimension number that indexes samples; see Examples. The default, MARGIN = 2, corresponds to columns of x indexing samples.

Details

The difference between calling DSArray() without any arguments and calling new("DSArray") is like the difference between calling array() and calling new("array"); using the explicit constructor is to be preferred.

Value

A DSArray object.

Dimnames

If the dimnames argument to the DSArray constructor is NULL then the dimnames of the returned DSArray object are constructed as follows:

• If x is an array: use dimnames(x)[MARGIN] for slicenames, and dimnames(x)[-MARGIN] as rownames and colnames of the returned object, respectively.

• If x is a list of matrix objects with identical dimensions: rownames of the returned object are the rownames of the first element x with non-NULL rownames; colnames of the returned object are taken from names(x); slicenames of the returned object are the colnames of first element of x with non-NULL colnames.

• If x is a matrix: use rownames(x) for the rownames and colnames(x) for the slicenames of the returned object, respectively. The colnames of the returned object are NULL.

Author(s)

Peter Hickey

See Also

DSArray-class

Examples

# Constructing a DSArray from matrix input
m <- matrix(1:10, ncol = 2, dimnames = list(letters[1:5], LETTERS[1:2]))
m
m_dsa <- DSArray(m)
m_dsa
# Supplying alternate dimnames
DSArray(m, dimnames = list(rownames(m), "sample-1", colnames(m)))

PeteHaitch/DSArray documentation built on May 8, 2019, 1:30 a.m.