ctgGEMset: The ctgGEMset class

In bicbioeng/ctgGEM: Generating Tree Hierarchy Visualizations from Gene Expression Data

Description

The main class used by the cellTreeGenerator package to hold single cell gene expression data and generated tree results. ctgGEMset extends the SummarizedExperiment::SummarizedExperiment class.

Usage

ctgGEMset(exprsData, phenoData = NULL, featureData = NULL)

Arguments

exprsData	expression data matrix for an experiment
phenoData	a data frame containing attributes of individual samples
featureData	a data frame containing attributes of features (genes)

Details

This class is initialized from a matrix of gene expression values and associated metadata. Methods that operate on ctgGEMset objects comprise the ctgGEM workflow.

Value

a new ctgGEMset object

Fields

monocleInfo

A character vector of parameters used by generate_tree(treeType = "monocle") in the cellTreeGenerator workflow

TSCANinfo

A character vector of the row name of a single gene in exprsData() to use for a single gene vs. pseudotime plot for generate_tree(treeType = "TSCAN") in the cellTreeGenerator workflow

sincellInfo

A list containing named parameters used by generate_tree(treeType = "sincell") in the cellTreeGenerator workflow

treeList

A list containing the simplified igraph representation of the trees generated by the ctgGEM workflow

originalTrees

A list containing the trees generated by the ctgGEM workflow in their original formats for re-plotting

Examples

# load HSMMSingleCell package
library(HSMMSingleCell)

# load the data
data(HSMM_expr_matrix)
data(HSMM_sample_sheet)
data(HSMM_gene_annotation)

# construct a ctgGEMset
dataSet <- ctgGEMset(exprsData = HSMM_expr_matrix,
                        phenoData = HSMM_sample_sheet,
                        featureData = HSMM_gene_annotation)
# load HSMMSingleCell package
library(HSMMSingleCell)

# load the data
data(HSMM_expr_matrix)
data(HSMM_sample_sheet)
data(HSMM_gene_annotation)


# construct a ctgGEMset
dataSet <- ctgGEMset(exprsData = HSMM_expr_matrix,
                        phenoData = HSMM_sample_sheet,
                        featureData = HSMM_gene_annotation)

bicbioeng/ctgGEM documentation built on Sept. 5, 2021, 8:42 p.m.