ctgGEMset {ctgGEM}R Documentation

The ctgGEMset class

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

cellTreeInfo

a character vector of the name of the column of phenoData() to use for grouping data for generate_tree(treeType = "cellTree") in the cellTreeGenerator workflow

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)
[Package ctgGEM version 0.99.3 Index]