View source: R/differential_expression.R
diff_gene_list | R Documentation |
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, ... )
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 ≥ 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.
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".
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