From 4a28eaa04c5e9172979d70949f201eb475f25557 Mon Sep 17 00:00:00 2001 From: JoseCorCab Date: Fri, 26 Jul 2024 09:18:06 +0200 Subject: [PATCH] correlation Pvalue cutoff for PCA loadings has been disables --- R/main_functional_hunter.R | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/R/main_functional_hunter.R b/R/main_functional_hunter.R index b8694ec..4a9c40d 100644 --- a/R/main_functional_hunter.R +++ b/R/main_functional_hunter.R @@ -145,7 +145,7 @@ main_functional_hunter <- function( # prepare PCA data for KS pca_eigenvectors <- lapply(hunter_results$pca_data, get_and_parse_pca_eigenvectors, - cor_pval = 0.05, + cor_pval = 1, eig_abs_cutoff = NULL) } @@ -204,7 +204,17 @@ main_functional_hunter <- function( if (!is.null(hunter_results$pca_data)) { - func_results$PCA_enrichments <- lapply(pca_eigenvectors, multienricher_topGO, all_funsys = enrich_dbs,organism_info = current_organism_info,p_value_cutoff = pthreshold,algorithm = "classic",statistic = "t",gene_id = "ensembl", scoreOrder = "decreasing",workers = cores, task_size = task_size) + func_results$PCA_enrichments <- lapply(pca_eigenvectors, + multienricher_topGO, + all_funsys = enrich_dbs, + organism_info = current_organism_info, + p_value_cutoff = pthreshold, + algorithm = "classic", + statistic = "t", + gene_id = "ensembl", + scoreOrder = "decreasing", + workers = cores, + task_size = task_size) } ############################################################ ## ##