markerDiffTable: Test genes for cell type-dependent expression

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

takes a CellDataSet and a CellTypeHierarchy and classifies all cells into types passed functions passed into the CellTypeHierarchy. The function will remove all "Unknown" and "Ambiguous" types before identifying genes that are differentially expressed between types.

Usage

markerDiffTable(cds, cth, residualModelFormulaStr = "~1", balanced = FALSE,
  reclassify_cells = TRUE, remove_ambig = TRUE, remove_unknown = TRUE,
  verbose = FALSE, cores = 1)

Arguments

cds	A CellDataSet object containing cells to classify
cth	The CellTypeHierarchy object to use for classification
residualModelFormulaStr	A model formula string specify effects you want to exclude when testing for cell type dependent expression
balanced	Whether to downsample the cells so that there's an equal number of each type prior to performing the test
reclassify_cells	a boolean that indicates whether or not the cds and cth should be run through classifyCells again
remove_ambig	a boolean that indicates whether or not ambiguous cells should be removed the cds
remove_unknown	a boolean that indicates whether or not unknown cells should be removed from the cds
verbose	Whether to emit verbose output during the the search for cell-type dependent genes
cores	The number of cores to use when testing

Value

A table of differential expression test results

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.