newCellDataSet: Creates a new CellDateSet object.

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Creates a new CellDateSet object.

Usage

newCellDataSet(cellData, phenoData = NULL, featureData = NULL,
  lowerDetectionLimit = 0.1, expressionFamily = VGAM::negbinomial.size())

Arguments

cellData	expression data matrix for an experiment
phenoData	data frame containing attributes of individual cells
featureData	data frame containing attributes of features (e.g. genes)
lowerDetectionLimit	the minimum expression level that consistitutes true expression
expressionFamily	the VGAM family function to be used for expression response variables

Value

a new CellDataSet object

Examples

## Not run: 
sample_sheet_small <- read.delim("../data/sample_sheet_small.txt", row.names=1)
sample_sheet_small$Time <- as.factor(sample_sheet_small$Time)
gene_annotations_small <- read.delim("../data/gene_annotations_small.txt", row.names=1)
fpkm_matrix_small <- read.delim("../data/fpkm_matrix_small.txt")
pd <- new("AnnotatedDataFrame", data = sample_sheet_small)
fd <- new("AnnotatedDataFrame", data = gene_annotations_small)
HSMM <- new("CellDataSet", exprs = as.matrix(fpkm_matrix_small), phenoData = pd, featureData = fd)

## End(Not run)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.