newSCESet {scater} | R Documentation

## Create a new SCESet object

### Description

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.

### Usage

    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)

### Arguments

`exprsData` | expression data matrix for an experiment (features x cells)
`countData` | data matrix containing raw count expression values
`tpmData` | matrix of class `"numeric"` containing transcripts-per-million (TPM) expression values
`fpkmData` | matrix of class `"numeric"` containing fragments per kilobase of exon per million reads mapped (FPKM) expression values
`cpmData` | matrix of class `"numeric"` containing counts per million (CPM) expression values (optional)
`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 `"logical"`, indicating whether or not each observation is above the `lowerDetectionLimit`.
`cellPairwiseDistances` | object of class `"dist"` (or a class that extends "dist") containing cell-cell distance or dissimilarity values.
`featurePairwiseDistances` | object of class `"dist"` (or a class that extends "dist") containing feature-feature distance or dissimilarity values.
`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 `1`.

### Details

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`.

### Value

a `SingleCellExperiment` object

### Examples

    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)

[Package scater version 1.6.3 Index]