TF activity inference working

.gitignore

@@ -12,3 +12,6 @@
 
 # R project file
 easier.Rproj
+
+# Omnipath log
+omnipathr-log/

DESCRIPTION

@@ -61,12 +61,13 @@ Imports:
     rstatix,
     ggrepel,
     magrittr,
-    coin
+    coin,
+    OmnipathR
 Suggests: 
-    knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper
+    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: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

NAMESPACE

@@ -25,7 +25,8 @@ importFrom(ROCR,performance)
 importFrom(ROCR,plot)
 importFrom(ROCR,prediction)
 importFrom(coin,pvalue)
-importFrom(decoupleR,run_viper)
+importFrom(decoupleR,get_collectri)
+importFrom(decoupleR,run_wmean)
 importFrom(dplyr,filter)
 importFrom(easierData,get_HGNC_annotation)
 importFrom(easierData,get_TCGA_mean_pancancer)
@@ -42,7 +43,6 @@ importFrom(ggpubr,ggarrange)
 importFrom(ggpubr,text_grob)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,recordPlot)
-importFrom(graphics,abline)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,par)
@@ -53,11 +53,9 @@ importFrom(progeny,getModel)
 importFrom(progeny,progeny)
 importFrom(quantiseqr,run_quantiseq)
 importFrom(reshape2,melt)
-importFrom(rlang,.data)
 importFrom(rstatix,wilcox_effsize)
 importFrom(rstatix,wilcox_test)
 importFrom(stats,aggregate)
-importFrom(stats,cor)
 importFrom(stats,median)
 importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
@@ -67,8 +65,6 @@ importFrom(stats,sd)
 importFrom(stats,var)
 importFrom(tibble,column_to_rownames)
 importFrom(tidyr,pivot_wider)
-importFrom(utils,View)
 importFrom(utils,combn)
-importFrom(utils,data)
 importFrom(utils,head)
 importFrom(utils,tail)

R/compute_TF_activity.R

@@ -12,6 +12,7 @@
 #'
 #' @import magrittr
 #' @importFrom stats na.exclude
+#' @importFrom dplyr filter
 #' @importFrom decoupleR get_collectri run_wmean
 #' @importFrom tidyr pivot_wider
 #' @importFrom tibble column_to_rownames
@@ -81,7 +82,7 @@ compute_TF_activity <- function(RNA_tpm = NULL,
   # collectTRI network
   net <- decoupleR::get_collectri(organism='human', split_complexes=FALSE)
   all_regulated_transcripts <- unique(net$target)
-  all_tfs <- unique(net$tf)
+  all_tfs <- unique(net$source)
 
   # check what is the percentage of genes we have in our data
   genes_kept <- intersect(rownames(E), all_regulated_transcripts)
@@ -103,12 +104,13 @@ compute_TF_activity <- function(RNA_tpm = NULL,
   # TF activity: run viper
   tf_activity_df <- decoupleR::run_wmean(mat = E,
                                          net = net,
-                                         .source='tf',
+                                         .source='source',
                                          .target='target',
                                          .mor='mor', 
                                          minsize = 5)
   # To matrix
   tf_activity <- tf_activity_df %>%
+    dplyr::filter(statistic == "wmean") %>%
     tidyr::pivot_wider(id_cols = condition,
                        names_from = source,
                        values_from = score) %>%

R/easier-package.R

@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

vignettes/easier_user_manual.Rmd

@@ -166,6 +166,7 @@ suppressPackageStartupMessages({
 For this example we will use gene expression data (counts and tpm values). Other variables include patient best overall response (BOR) to anti-PD-L1 therapy, tumor mutational burden (TMB) and the cancer type the cohort belongs to.
 
 ```{r, eval=TRUE}
+
 dataset_mariathasan <- get_Mariathasan2018_PDL1_treatment()
 
 # patient response