newCellDataSet {monocle}R Documentation

Creates a new CellDateSet object.

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)

[Package monocle version 2.18.0 Index]