waveST-class: S4 Class for a waveST

In OliverXUZY/waveST: Wavelet-Based Spatial Transcriptomic Dimensionality Reduction

S4 Class for a waveST

Description

The waveST class stores the data and additional result after computing.

Details

If spatial is not given, the class assumes the data is generated input: location(D^2)-by-gene(2). The class set input = data, this is useful when we already have location(D^2)-by-gene(2) matrix (like settings in simulations).

      The content of \code{output} depends on whether use wavelet, and the decomposition methods.
      The  \code{output} is NA once created. The values will be updated once called \code{\link{decompse}}.

Slots

data

original data, cell(n)-by-gene(p) matrix, can be matrix/data.frame/tibble

spatial

cell(n)-by-location(2) matrix, representing coordinates of each cell, see "details"

input

location(D^2)-by-gene(2) matrix, representing gene expression over location

output

a list containing SVD-like output: factors, diagonal matrix, loadings, fitted values, see "details"

Note

The decomposition in this package require a waveST input.

Author(s)

Zhuoyan Xu [e-mail]

Examples

wave = new("waveST", data = matrix(rnorm(6), 2, 3))

OliverXUZY/waveST documentation built on June 9, 2024, 6:18 a.m.