TestData: TestData: A test scRNA-seq real dataset for SwarnSeq

In sam-uofl/SwarnSeq: Detection of Differentially Expressed Genes from Single Cell RNA-seq Data

Description

A toy dataset containing a single-cell RNA-seq (scRNA-seq) read counts matrix, ERCC spike-ins counts and spike-in concentration.

Usage

data(TestData)

Format

• CountData. A matrix of raw read counts of scRNA-seq data which has 500 genes (rows) and 200 cells (columns).

• SpikeCounts. A matrix of read counts for spik-in transcripts to estimate the capture efficiencies of the cells.

• SpikeConc. A vector of the molecular concentration for spike-in transcripts.

• group. A vector specifying the two groups and can be generated by: group <- c(rep(1,100), rep(2,100)).

• CellCluster. A vector specifying the cell cluster memberships of the cells in CountData and for example can be generated by: CellCluster <- c(rep(1,20), rep(2,30), rep(3, 40), rep(4, 50), rep(5, 60)).

Details

• CountData. A matrix of raw read counts of scRNA-seq data which has 200 genes (rows) and 200 cells (columns).

• SpikeCounts. A matrix of read counts for spik-in transcripts to estimate the capture efficiencies of the cells.

• SpikeConc. A vector of the molecular concentration for spike-in transcripts.

• group. A vector specifying the two groups and can be generated by: group <- c(rep(1,100), rep(2,100))

• CellCluster. A vector specifying the cell cluster memberships of the cells in CountData and for example can be generated by: CellCluster <- c(rep(1,20), rep(2,30), rep(3, 40), rep(4, 50), rep(5, 60)).

Source

Petropoulos S, et al. Cell, 2016, 165(4): 1012-1026.

Examples

# Load test data for DEsingle

data(TestData)
CountData = TestData$CountData
SpikeCounts = TestData$SpikeCounts
SpikConc = TestData$SpikeConc

# Specifying the two groups to be compared
# The sample number in group 1 and group 2 is 100 and 100 cells respectively
group <- c(rep(1,100), rep(2,100))

# Specifying the cluster-memberships of the cells.
CellCluster <- c(rep(1,20), rep(2,30), rep(3, 40), rep(4, 50), rep(5, 60))

sam-uofl/SwarnSeq documentation built on Sept. 6, 2020, 12:09 a.m.