ctgGEMset-methods {ctgGEM} | R Documentation |
These methods operate on ctgGEMset objects. Please note that treeList<- and originalTrees<- are not intended to be called directly.
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
cs |
A ctgGEMset object |
pt |
The name of the monocle or sincell parameter to store |
value |
|
tt |
The type of tree being stored |
An updated ctgGEMset object, or the contents of a slot of the ctgGEMset object
# 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)