This function returns a data frame with differential expression analysis results.
diff_gene_list(
data,
final_clust_res = NULL,
clust1 = "1",
clust2 = "2",
t_test = FALSE,
...
)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".
A departure matrix generated from adj_CDF_logit() or an S3 object for class 'scppp'.
A data frame with clustering results generated from HclustDepart(). It contains two columns: names (cell names) and clusters (cluster label).
One of the cluster label used to make comparison, default "1".
The other cluster label used to make comparison, default "2".
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.
This is a function used to find deferentially expressed genes between two clusters.