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 2.12.0 Index]