LinseedObject: Linseed Object

In ctlab/LinSeed: Linear Subpsace identification to solve complete gene expression deconvolution problem

Description

The Linseed Object Class.

Usage

LinseedObject

Format

R6Class object.

Details

Provides an interface to perform collinear network construction, linear subspace identification, simplex corner identification and gene expression deconvolution

Value

Object of R6Class – an interface to work with gene expression data.

Fields

exp

List of two elements raw and normalized gene expression dataset

name

Character, optional, dataset name

cellTypeNumber

Identified cell type number, required for projection, corner detection and deconvolution

projection

Projection of genes into space lower-dimensionality (presumably simplex)

endpoints

Simplex corners (in normalized, non-reduced space)

endpointsProjection

Simplex corners (in reduced space)

distances

Stores distances for every gene to each corner in reduced space

markers

List that stores signatures genes for deconvolution, can be set manually or can be obtained by selectGenes(k)

signatures

Deconvolution signature matrix

proportions

Deconvolution proportion matrix

pairwise

Calculated pairwise collinearity measure

Examples

LinseedObject$new("GSE19830", samples=10:42, topGenes=10000)

ctlab/LinSeed documentation built on Aug. 9, 2019, 4:33 p.m.