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]