check corrected

seoanezonjic · Jan 24, 2024 · 493f32b · 493f32b
1 parent 1d6cb33
commit 493f32b
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Showing 3 changed files with 5 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -110,5 +110,6 @@ Imports:
     clusterProfiler,
     GenomicRanges,
     annotatr,
-    ggridges
+    ggridges,
+    FactoInvestigate
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -40,6 +40,8 @@ importFrom(DESeq2,results)
 importFrom(DESeq2,rlog)
 importFrom(DOSE,setReadable)
 importFrom(DT,datatable)
+importFrom(FactoInvestigate,dimRestrict)
+importFrom(FactoInvestigate,eigenRef)
 importFrom(GO.db,GOBPANCESTOR)
 importFrom(GO.db,GOBPPARENTS)
 importFrom(GO.db,GOCCANCESTOR)

diff --git a/R/statistics_functions.R b/R/statistics_functions.R
@@ -324,6 +324,7 @@ filter_and_integrate_OR <- function(cont_table, p.adjust.method = "BH" ,p_thr =
   return(list(integrated_stats = integrated_stats, miRNA_ct = miRNA_ct))
 }
 
+#' @importFrom FactoInvestigate dimRestrict eigenRef
 get_PCA_dimensions <- function(pca_obj, min_dimensions = 2) {
     ref = FactoInvestigate::eigenRef(pca_obj, time = "10s", parallel=FALSE) # to avoid use parallel computation that greedy takes all cpu cores
     rand = c(ref$inertia[1], diff(ref$inertia)) * 100