newCellDataSet {monocle} | R Documentation |
Creates a new CellDateSet object.
newCellDataSet( cellData, phenoData = NULL, featureData = NULL, lowerDetectionLimit = 0.1, expressionFamily = VGAM::negbinomial.size() )
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 |
a new CellDataSet object
## 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)