diff_gene_list {scpoisson}

Differential expression analysis

Description

This function returns a data frame with differential expression analysis results.

Usage

diff_gene_list(
  data,
  final_clust_res = NULL,
  clust1 = "1",
  clust2 = "2",
  t_test = FALSE,
  ...
)

Arguments

data

A departure matrix generated from adj_CDF_logit() or an S3 object for class 'scppp'.

final_clust_res

A data frame with clustering results generated from HclustDepart(). It contains two columns: names (cell names) and clusters (cluster label).

clust1

One of the cluster label used to make comparison, default "1".

clust2

The other cluster label used to make comparison, default "2".

t_test

A logical value indicating whether the t-test should be used to make comparison. In general, for large cluster (n \ge 30), the t-test should be used. Otherwise, the Wilcoxon test might be more appropriate.

...

not used.

Details

This is a function used to find deferentially expressed genes between two clusters.

Value

A data frame contains genes (ranked by decreasing order of mean difference), and associated statistics (p-values, FDR adjusted p-values, etc.). If the input is an S3 object for class 'scppp', differential expression analysis results will be stored in object scppp under "de_results".