newSCESet {scater} | R Documentation |
Deprecated from scater version 1.3.29; the package now uses the
SingleCellExperiment
class. To convert an SCESet object to
SingleCellExperiment see the toSingleCellExperiment
function.
This function is retained for backwards compatibility.
newSCESet(exprsData = NULL, countData = NULL, tpmData = NULL, fpkmData = NULL, cpmData = NULL, phenoData = NULL, featureData = NULL, experimentData = NULL, is_exprsData = NULL, cellPairwiseDistances = dist(vector()), featurePairwiseDistances = dist(vector()), lowerDetectionLimit = NULL, logExprsOffset = NULL)
exprsData |
expression data matrix for an experiment (features x cells) |
countData |
data matrix containing raw count expression values |
tpmData |
matrix of class |
fpkmData |
matrix of class |
cpmData |
matrix of class |
phenoData |
data frame containing attributes of individual cells |
featureData |
data frame containing attributes of features (e.g. genes) |
experimentData |
MIAME class object containing metadata data and details about the experiment and dataset. |
is_exprsData |
matrix of class |
cellPairwiseDistances |
object of class |
featurePairwiseDistances |
object of class |
lowerDetectionLimit |
the minimum expression level that constitutes true expression (defaults to zero and uses count data to determine if an observation is expressed or not). |
logExprsOffset |
numeric scalar, providing the offset used when doing
log2-transformations of expression data to avoid trying to take logs of zero.
Default offset value is |
This function now returns a SingleCellExperiment
object,
whereas earlier versions produced an SCESet
object. The scater
package now uses SingleCellExperiment
as its data structure instead
of SCESet
.
a SingleCellExperiment
object
data("sc_example_counts") data("sc_example_cell_info") pd <- new("AnnotatedDataFrame", data = sc_example_cell_info) ## Not run: example_sce <- newSCESet(countData = sc_example_counts, phenoData = pd) ## End(Not run)