Description Usage Arguments Value Author(s) See Also Examples

This function is used to detect differentially expressed genes between two specified groups of cells in a raw read counts matrix of single-cell RNA-seq (scRNA-seq) data. It takes a non-negative integer matrix of scRNA-seq raw read counts or a `SingleCellExperiment`

object as input. So users should map the reads (obtained from sequencing libraries of the samples) to the corresponding genome and count the reads mapped to each gene according to the gene annotation to get the raw read counts matrix in advance.

1 |

`counts` |
A non-negative integer matrix of scRNA-seq raw read counts or a |

`group` |
A vector of factor which specifies the two groups to be compared, corresponding to the columns in the counts matrix. |

`parallel` |
If FALSE (default), no parallel computation is used; if TRUE, parallel computation using |

`BPPARAM` |
An optional parameter object passed internally to |

A data frame containing the differential expression (DE) analysis results, rows are genes and columns contain the following items:

theta_1, theta_2, mu_1, mu_2, size_1, size_2, prob_1, prob_2: MLE of the zero-inflated negative binomial distribution's parameters of group 1 and group 2.

total_mean_1, total_mean_2: Mean of read counts of group 1 and group 2.

foldChange: total_mean_1/total_mean_2.

norm_total_mean_1, norm_total_mean_2: Mean of normalized read counts of group 1 and group 2.

norm_foldChange: norm_total_mean_1/norm_total_mean_2.

chi2LR1: Chi-square statistic for hypothesis testing of H0.

pvalue_LR2: P value of hypothesis testing of H20 (Used to determine the type of a DE gene).

pvalue_LR3: P value of hypothesis testing of H30 (Used to determine the type of a DE gene).

FDR_LR2: Adjusted P value of pvalue_LR2 using Benjamini & Hochberg's method (Used to determine the type of a DE gene).

FDR_LR3: Adjusted P value of pvalue_LR3 using Benjamini & Hochberg's method (Used to determine the type of a DE gene).

pvalue: P value of hypothesis testing of H0 (Used to determine whether a gene is a DE gene).

pvalue.adj.FDR: Adjusted P value of H0's pvalue using Benjamini & Hochberg's method (Used to determine whether a gene is a DE gene).

Remark: Record of abnormal program information.

Zhun Miao.

`DEtype`

, for the classification of differentially expressed genes found by `DEsingle`

.

`TestData`

, a test dataset for DEsingle.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
# 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)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.