In OceaneCsn/DIANE: DIANE

r <- params$r_dea
the_r <- params$r
library(knitr)

Dashboard for the Inference and Analysis of Networks from Expression data

This report was automatically generated by DIANE to improve research reproducibility.

It contains the main settings and results for the DEA tab of the application, reporting the last transcriptome comparison that was performed.

Your settings

Normalization method :

print(the_r$norm_method)

Reference and perturbation condition :

paste(r$ref, r$trt)

Threshold adjusted p-value and minimal expected absolute log fold change :

paste("FDR =", r$fdr, "LFC = ", r$lfc)

Results

Number of up-regulated genes :

nrow(r$gene_table[r$gene_table$Regulation == "Up",])

Number of down-regulated genes :

nrow(r$gene_table[r$gene_table$Regulation == "Down",])

DEGs table :

DT::datatable(r$gene_table)

The entire table is downloadable from the application as a csv file.

Plots

DIANE::draw_DEGs(r$tags, fdr = r$fdr, lfc = r$lfc, MA = TRUE)
DIANE::draw_DEGs(r$tags, fdr = r$fdr, lfc = r$lfc, MA = FALSE)
DIANE::draw_heatmap(r$gene_table$genes, data = the_r$normalized_counts, title = paste(r$ref, "versus", r$trt), conditions = c(r$ref, r$trt))