TestData: TestData: A test dataset for DEsingle

In DEsingle: DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Description

A toy dataset containing a single-cell RNA-seq (scRNA-seq) read counts matrix and its grouping information.

Usage

data(TestData)

Format

• counts. A non-negative integer matrix of scRNA-seq raw read counts, rows are genes and columns are cells.

• group. A vector of factor specifying the two groups to be compared, corresponding to the columns of the counts.

Details

• counts. A matrix of raw read counts of scRNA-seq data which has 200 genes (rows) and 150 cells (columns).

• group. A vector of factor specifying the two groups to be compared in counts. Also could be generated by: group <- factor(c(rep(1,50), rep(2,100)))

Source

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

See Also

DEsingle, for the detection of differentially expressed genes from scRNA-seq data.

DEtype, for the classification of differentially expressed genes found by DEsingle.

Examples

# Load test data for DEsingle
data(TestData)

# Specifying the two groups to be compared
# The sample number in group 1 and group 2 is 50 and 100 respectively
group <- factor(c(rep(1,50), rep(2,100)))

# Detecting the differentially expressed genes
results <- DEsingle(counts = counts, group = group)

# Dividing the differentially expressed genes into 3 categories
results.classified <- DEtype(results = results, threshold = 0.05)

DEsingle documentation built on Nov. 8, 2020, 7:17 p.m.