Release 3 17

DESCRIPTION

@@ -41,6 +41,7 @@ Imports:
     progeny,
     easierData,
     dorothea (>= 1.6.0),
+    decoupleR,
     quantiseqr,
     ROCR,
     grDevices, 
@@ -51,18 +52,21 @@ Imports:
     DESeq2,
     utils,
     dplyr,
+    tidyr,
+    tibble,
     matrixStats,
     rlang,
     BiocParallel,
     reshape2,
     rstatix,
     ggrepel,
+    magrittr,
     coin
 Suggests: 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
 biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NAMESPACE

@@ -13,6 +13,7 @@ export(explore_biomarkers)
 export(predict_immune_response)
 export(retrieve_easier_score)
 import(ggplot2)
+import(magrittr)
 importFrom(BiocParallel,MulticoreParam)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,register)
@@ -24,7 +25,7 @@ importFrom(ROCR,performance)
 importFrom(ROCR,plot)
 importFrom(ROCR,prediction)
 importFrom(coin,pvalue)
-importFrom(dorothea,run_viper)
+importFrom(decoupleR,run_viper)
 importFrom(dplyr,filter)
 importFrom(easierData,get_HGNC_annotation)
 importFrom(easierData,get_TCGA_mean_pancancer)
@@ -64,6 +65,8 @@ importFrom(stats,prcomp)
 importFrom(stats,quantile)
 importFrom(stats,sd)
 importFrom(stats,var)
+importFrom(tibble,column_to_rownames)
+importFrom(tidyr,pivot_wider)
 importFrom(utils,View)
 importFrom(utils,combn)
 importFrom(utils,data)

R/compute_LR_pairs.R

@@ -166,6 +166,8 @@ compute_LR_pairs <- function(RNA_tpm = NULL,
     colnames(LR_pairs_computed)[pos_keep] <- combo_name
     LR_pairs_computed <- LR_pairs_computed[, -pos_remove]
   }
+  # Remove LR pairs with all NA values
+  LR_pairs_computed <- LR_pairs_computed[, !is.na(apply(LR_pairs_computed, 2, sum))]
 
   if (verbose) message("Ligand-Receptor pair weights computed \n")
   return(as.data.frame(LR_pairs_computed))

R/compute_TF_activity.R

@@ -10,9 +10,12 @@
 #' the estimation of human transcription factor activities."
 #' Genome Research. 2019. DOI: 10.1101/gr.240663.118.
 #'
-#' @importFrom dorothea run_viper
+#' @import magrittr
 #' @importFrom stats na.exclude
 #' @importFrom dplyr filter
+#' @importFrom decoupleR run_viper
+#' @importFrom tidyr pivot_wider
+#' @importFrom tibble column_to_rownames
 #' @importFrom easierData get_TCGA_mean_pancancer get_TCGA_sd_pancancer
 #'
 #' @param RNA_tpm data.frame containing TPM values with HGNC symbols
@@ -93,17 +96,25 @@ compute_TF_activity <- function(RNA_tpm = NULL,
       round(length(genes_kept) / length(all_regulated_transcripts), 3) * 100, "%)"
     )
   }
-  # TF activity: run viper
-  tf_activity <- dorothea::run_viper(
-    input = E, regulons = regulons,
-    options = list(
-      method = "none", minsize = 4, eset.filter = FALSE,
-      cores = 1, verbose = FALSE
-    )
-  )
 
-  # Samples as rows, TFs as columns
-  tf_activity <- t(tf_activity)
+  # Remove genes with all NA/Inf values
+  E <- E[!is.na(apply(E, 1, sum)), ]
+  E <- E[!is.infinite(apply(E, 1, sum)), ]
+
+  # TF activity: run viper
+  tf_activity_df <- decoupleR::run_viper(mat = E,
+                                         network = regulons,
+                                         .source = "tf",
+                                         minsize = 4,
+                                         eset.filter = FALSE,
+                                         method = "none",
+                                         verbose = FALSE)
+  # To matrix
+  tf_activity <- tf_activity_df %>%
+    tidyr::pivot_wider(id_cols = condition,
+                       names_from = source,
+                       values_from = score) %>%
+    tibble::column_to_rownames("condition")
 
   if (verbose) message("TF activity computed! \n")
 

vignettes/easier_user_manual.Rmd

@@ -59,7 +59,7 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup, include = FALSE}
-library("easier")
+#library("easier")
 ```
 
 # Introduction {#introduction}