newSCESet: Create a new SCESet object

Description Usage Arguments Details Value Examples

View source: R/SCESet-methods.R

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

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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

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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)

scater documentation built on Nov. 17, 2017, 10:54 a.m.