example_data: Example data

In CSCDRNA: Covariance Based Single-Cell Decomposition of Bulk Expression Data

Example data

Description

An example data containing synthetic bulk and single-cell datasets. This example illustrates how to build ExpressionSets and run CSCD.

Usage

example_data

Format

A list. Slot bulk.matrix contains a sample bulk data matrix with 100 rows (genes) and 5 columns (individuals). Slot sc.counts.matrix contains a sample single-cell data matrix with 100 rows (genes) and 20 columns (a combination of cells assigned to 4 different cell types and 5 individuals). Slot individual.labels contains individual labels in the single-cell data. Slot cell.type.labels contains cell-type labels in the single-cell data. Slot sample.ids contains sample ids in the single-cell data. Note that individual.labels and cell.types should be in the same order as in sample.ids.

Examples

# Load example data.
data(example_data)

# Build ExpressionSet with bulk data.
bulk.eset <- Biobase::ExpressionSet(assayData = example_data$bulk.matrix)

# Build ExpressionSet with single-cell data.
sc.counts.matrix=example_data$sc.counts.matrix
individual.labels=example_data$individual.labels
cell.type.labels=example_data$cell.type.labels
sample.ids <- colnames(sc.counts.matrix)
# individual.labels and cell.types should be in the same order as in sample.ids.
sc.pheno <- data.frame(check.names=FALSE, check.rows=FALSE,
                       stringsAsFactors=FALSE,row.names=sample.ids,
                       SubjectName=individual.labels,cellType=cell.type.labels)
sc.meta <- data.frame(labelDescription=c("SubjectName","cellType"),
                      row.names=c("SubjectName","cellType"))
sc.pdata <- new("AnnotatedDataFrame",data=sc.pheno, varMetadata=sc.meta)
sc.eset <- Biobase::ExpressionSet(assayData=sc.counts.matrix,phenoData=sc.pdata)

# Run CSCD on the example data.
analysis <- CSCD(bulk.eset=bulk.eset,sc.eset= sc.eset,
                 min.p=0.3,markers=NULL,cell.types="cellType",
                 subj.names="SubjectName",verbose=TRUE)

# Estimated cell-type proportions.
analysis$bulk.props

# Cell-type proportions estimated directly by counting single-cell data.
analysis$sc.props

# The covariance based transformed bulk expression used for decomposition.
analysis$transformed.bulk.

# Genes used in the decomposition.
analysis$genes.used

# Euclidean norm of the residuals for each individual's proportion estimates.
analysis$rnorm

CSCDRNA documentation built on June 24, 2022, 5:05 p.m.