diff --git a/inst/templates/global_cormit.Rmd b/inst/templates/global_cormit.Rmd index 63fa370..6f1d4e6 100644 --- a/inst/templates/global_cormit.Rmd +++ b/inst/templates/global_cormit.Rmd @@ -151,7 +151,10 @@ This section describes the optimal pairs for each miRNA were selected through th ```{r overall_results_table, echo=FALSE, results = 'asis', warning = FALSE, message = FALSE, fig.width = 4, fig.height = 4} overall_stats <- all_pairs[!is.na(all_pairs$normalized_counts_RNA_vs_miRNA_normalized_counts_correlation),] - int_stats <- overall_stats[overall_stats$integrated_strat,] + overall_stats$miRNA <- mirna_names[match(overall_stats$miRNAseq, mirna_names$ACCESSION), "NAME"] + + int_stats <- overall_stats[overall_stats$miRNA %in% unique(miRNA_cont_tables[miRNA_cont_tables$db_group == "multimir", "miRNA"]),] + int_stats <- int_stats[int_stats$integrated_strat,] overall_summary <- data.frame("Input miRNA" = length(unique(overall_stats$miRNAseq)), "Input RNA" = length(unique(overall_stats$RNAseq)), "miRNA with targets" = length(unique(int_stats$miRNAseq)), @@ -200,8 +203,9 @@ miRNA_cont_tables_mult$strategy <- set_strats_readable(miRNA_cont_tables_mult$st This table shows different statistics about optimal strategy for each miRNA. ```{r best_strat_mult, echo=FALSE, results = 'asis', warning = FALSE, message = FALSE} -best_strats_to_print <- best_strats_mult[,c("miRNA","strategy","Odds_ratio", "corr_cutoff", "p.adjust")] -colnames(best_strats_to_print) <- c("miRNA","Strategy","Specific Odds Ratio", "Correlation cutoff", "Fisher's exact test FDR") + +best_strats_to_print <- best_strats_mult[,c("miRNA","strategy","TP", "Odds_ratio", "corr_cutoff", "p.adjust")] +colnames(best_strats_to_print) <- c("miRNA","Strategy","Pairs in DBs", "Specific Odds Ratio", "Correlation cutoff", "Fisher's exact test FDR") knitr::kable(best_strats_to_print) ```