ctgGEMset-methods {ctgGEM} | R Documentation

## Methods for the ctgGEMset class

### Description

These methods operate on ctgGEMset objects. Please note that treeList<- and originalTrees<- are not intended to be called directly.

### Usage

    cellTreeInfo(cs)

    cellTreeInfo(cs) <- value

    monocleInfo(cs)

    monocleInfo(cs, pt) <- value

    TSCANinfo(cs)

    TSCANinfo(cs) <- value

    sincellInfo(cs)

    sincellInfo(cs, pt) <- value

    treeList(cs)

    treeList(cs, tt) <- value

    originalTrees(cs)

    originalTrees(cs, tt) <- value

### Arguments

`cs` | A ctgGEMset object
`value` | `cellTreeInfo(cs)<-`: A character vector of the name of the column of `phenoData()` to use for grouping data `monocleInfo(cs)<-`: The value to use as a named parameter for `generate_tree(treeType = "monocle")` `TSCANinfo(cs)<-`: 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")` `sincellInfo(cs)<-`: The value to use as a named parameter for sincell, used by `generate_tree(treeType = "sincell")`
`pt` | The name of the monocle or sincell parameter to store
`tt` | The type of tree being stored

### Value

An updated ctgGEMset object, or the contents of a slot of the ctgGEMset object

### 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)

    cellTreeInfo(dataSet) <- "Hours"
    cellTreeInfo(dataSet)

    monocleInfo(dataSet, "gene_id") <- "gene_short_name"
    monocleInfo(dataSet, "cell_id_1") <- "MYF5"
    monocleInfo(dataSet, "cell_id_2") <- "ANPEP"
    monocleInfo(dataSet, "ex_type") <- "FPKM"
    monocleInfo(dataSet)

    TSCANinfo(dataSet) <- "ENSG00000000003.10"
    TSCANinfo(dataSet)

    sincellInfo(dataSet, "method") <- "classical-MDS"
    sincellInfo(dataSet, "MDS.distance") <- "spearman"
    sincellInfo(dataSet, "clust.method") <- "k-medoids"
    sincellInfo(dataSet)

    # The following two examples will return empty lists, since no trees
    # have been generated on this ctgGEMset
    trees <- treeList(dataSet)
    originalTrees <- originalTrees(dataSet)

[Package ctgGEM version 0.99.3 Index]