ctgGEMset-methods: Methods for the ctgGEMset class

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

Description

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

Usage

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
pt	The name of the monocle or sincell parameter to store
value	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")
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)

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)

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