Add TIGER (#283)

* Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>

DESCRIPTION

@@ -27,6 +27,8 @@ Depends: R (>= 4.2.0),
          pandaR,
          yarn,
          matrixcalc
+Remotes: 
+	 stan-dev/cmdstanr 
 biocViews:
 	 NetworkInference,
 	 Network,
@@ -35,45 +37,50 @@ biocViews:
          Transcription, 
          Microarray,   
          GraphAndNetwork
-Imports: RCy3,
-	 viridisLite, 
-   STRINGdb,
-	 Biobase,
-	 GOstats,
-	 AnnotationDbi,
-   matrixStats,
-   GO.db,
-	 org.Hs.eg.db,
-	 Matrix,
-	 gplots,
-	 nnet,
-	 data.table,
-	 vegan,
-	 stats,
-	 utils,
-   reshape,
-   reshape2,
-   penalized,
-   parallel,
-   doParallel,
-   foreach,
-   ggplot2,
-   ggdendro,
-   grid,
-   MASS,
-   assertthat,
-   tidyr,
-   methods,
-   dplyr,
-   graphics
+Imports: 
+    RCy3,
+    viridisLite,
+    STRINGdb,
+    Biobase,
+    GOstats,
+    AnnotationDbi,
+    matrixStats,
+    GO.db,
+    org.Hs.eg.db,
+    Matrix,
+    gplots,
+    nnet,
+    data.table,
+    vegan,
+    stats,
+    utils,
+    reshape,
+    reshape2,
+    penalized,
+    parallel,
+    doParallel,
+    foreach,
+    ggplot2,
+    ggdendro,
+    grid,
+    MASS,
+    assertthat,
+    tidyr,
+    methods,
+    dplyr,
+    graphics,
+	cmdstanr,
+    GeneNet,
+    loo
 License: GPL-3
 Encoding: UTF-8
 LazyData: false
 Suggests: 
     testthat (>= 2.1.0),
     knitr,
     rmarkdown,
-    pkgdown
+    pkgdown,
+    dorothea
 VignetteEngine: knitr
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3

R/TIGER.R

@@ -51,6 +51,9 @@
 #' @export
 #'
 #' @examples
+#' data(TIGER_expr)
+#' data(TIGER_prior)
+#' TIGER(TIGER_expr,TIGER_prior)
 TIGER = function(expr,prior,method="VB",
                      signed=TRUE,baseline=TRUE,psis_loo = FALSE,
                      seed=123,out_path=NULL,out_size = 300,
@@ -67,6 +70,8 @@ TIGER = function(expr,prior,method="VB",
   if (signed){
     prior = prior.pp(prior[TF.name,TG.name],expr)
     P = prior
+    TF.name = rownames(P)
+    TG.name = colnames(P)
   }else{
     P = prior[TF.name,TG.name]
   }
@@ -173,7 +178,6 @@ TIGER = function(expr,prior,method="VB",
 #' @return An adjacency matrix with rows as TFs and columns as genes.
 #' @export
 #'
-#' @examples
 el2adj = function(el){
   el = as.data.frame(el)
   all.A = unique(el[,1])
@@ -194,7 +198,6 @@ el2adj = function(el){
 #' second column is gene name, and third column is edge weight.
 #' @export
 #'
-#' @examples
 adj2el = function(adj){
   el = matrix(NA,nrow(adj)*ncol(adj),3)
   el[,1]=rep(row.names(adj), ncol(adj))
@@ -216,7 +219,6 @@ adj2el = function(adj){
 #' @return A VIPER required regulon object
 #' @export
 #'
-#' @examples
 el2regulon = function(el) {
   regulon_list = split(el, el$from)
   viper_regulons = lapply(regulon_list, function(regulon) {
@@ -234,7 +236,6 @@ el2regulon = function(el) {
 #' @return A VIPER required regulon object.
 #' @export
 #'
-#' @examples
 adj2regulon = function(adj){
   el = adj2el(adj)
   el = el[el[,3]!=0,]
@@ -251,7 +252,6 @@ adj2regulon = function(adj){
 #' @return A filtered prior network (adjacency matrix).
 #' @export
 #'
-#' @examples
 prior.pp = function(prior,expr){
 
   # filter tfs and tgs
@@ -284,6 +284,28 @@ prior.pp = function(prior,expr){
 }
 
 
+#' TIGER example prior network
+#'
+#' @format ## `TIGER_prior`
+#' A prior network matrix with 14 rows (TFs) and 1772 columns (genes)
+#' 
+#' @source <https://zenodo.org/record/7425777>
+#' @name TIGER_prior
+#' @usage data(TIGER_prior)
+"TIGER_prior"
+
+#' TIGER example expression matrix
+#'
+#' @format ## `TIGER_expr`
+#' A gene expression matrix with 1780 rows (genes) and 16 columns (samples)
+#' 
+#' @source <https://zenodo.org/record/7425777>
+#' @name TIGER_expr
+#' @usage data(TIGER_expr)
+"TIGER_expr"
+
+
+
 
 # stan model, conditional likelihood
 TIGER_C <-

R/zzz.R

@@ -0,0 +1,9 @@
+
+.onLoad <- function(...) {
+  cmdstan_version <- cmdstanr::cmdstan_version(error_on_NA = FALSE)
+  if (is.null(cmdstan_version)) {
+    #stop("No CmdStan installation found. Run cmdstanr::install_cmdstan() to install.", call. = FALSE)
+    cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+    cmdstanr::install_cmdstan()
+  }
+}