ctgGEMset: The ctgGEMset class

Description Usage Arguments Details Value Fields Examples

View source: R/ctgGEMset-class.R

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

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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

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# 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 July 19, 2020, 12:42 a.m.