Add TensorQTL support to eQTL mapping function and update README

.gitignore

@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store

DESCRIPTION

@@ -1,20 +1,32 @@
 Package: FastGxC
 Title: Efficient and Powerful Software for Simulating Data and Detecting Context-specific eQTL Effects in Multi-context Genomic Studies
-Version: 0.0.0.9000
+Version: 0.0.1
 Authors@R: 
     person("Lena", "Krockenberger", , "lkrocken@g.ucla.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0002-5987-5496"))
-Description: Functions to run FastGxC decomposition and subsequent context-specific eQTL mapping with multiple testing adjustment. This software also can be used to simulate data and run eQTL mapping on toy examples.
-Suggests:
+Description: Functions to run FastGxC decomposition and subsequent context-specific eQTL mapping with multiple testing adjustment. This software can also simulate data and run eQTL mapping on toy examples.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.2.0)
+Imports:
+    devtools,
     dplyr,
     data.table,
     MatrixEQTL,
     mvtnorm,
     reshape2,
     magrittr,
-    TreeQTL
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+    reticulate,
+    Rcpp
+LinkingTo:
+    Rcpp
+Suggests:
+    qvalue,
+    TreeQTL,
+    TreeBH,
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -6,5 +6,18 @@ export(eQTL_mapping_step)
 export(get_eGenes_multi_tissue_mod)
 export(get_eSNPs_multi_tissue_mod)
 export(get_pvals_and_fam_p_mod)
+export(install_deps)
 export(simulate_data)
+export(to_TreeBH_input)
+export(treeBH_step)
 export(treeQTL_step)
+importFrom(Rcpp,sourceCpp)
+importFrom(data.table,fread)
+importFrom(data.table,getDTthreads)
+importFrom(data.table,setDTthreads)
+importFrom(dplyr,distinct)
+importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
+importFrom(dplyr,select)
+importFrom(magrittr,"%>%")
+useDynLib(FastGxC, .registration = TRUE)

R/RcppExports.R

@@ -0,0 +1,31 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' Check if groups are properly nested in hierarchy
+checkNested <- function(groups, L) {
+    .Call(`_FastGxC_checkNested`, groups, L)
+}
+
+#' Hierarchical Group P-value Calculation
+#' The getGroupPvalues function computes aggregated p-values for each group in a hierarchical 
+#' structure by combining p-values from lower levels using specified aggregation methods.
+#' @param pvals NumericVector containing p-values for individual hypotheses
+#' @param groups CharacterMatrix defining the group hierarchy structure
+#' @param N Integer specifying the number of hypotheses
+#' @param L Integer specifying the number of levels in the hierarchy
+#' @param test CharacterVector specifying the aggregation method(s)
+getGroupPvalues <- function(pvals, groups, N, L, test) {
+    .Call(`_FastGxC_getGroupPvalues`, pvals, groups, N, L, test)
+}
+
+#' Hierarchical Group Selection for Multiple Testing
+#' The getGroupSelections function applies hierarchical multiple testing correction.
+#' @param group_pvals NumericMatrix containing aggregated p-values
+#' @param groups CharacterMatrix defining the group hierarchy structure
+#' @param q NumericVector containing the q-value thresholds for each level
+#' @param N Integer specifying the number of hypotheses
+#' @param L Integer specifying the number of levels in the hierarchy
+getGroupSelections <- function(group_pvals, groups, q, N, L) {
+    .Call(`_FastGxC_getGroupSelections`, group_pvals, groups, q, N, L)
+}
+

R/deps.R

@@ -0,0 +1,46 @@
+# R/deps.R
+
+#' Install FastGxC dependencies
+#'
+#' Installs CRAN, Bioconductor, and source packages required by FastGxC.
+#' This includes optional packages like qvalue, TreeQTL, and TreeBH.
+#'
+#' @param ask Logical, whether to ask before installing (default: TRUE if interactive).
+#' @export
+install_deps <- function(ask = interactive()) {
+  # --- Core CRAN packages (should already install via Imports:) ---
+  cran_pkgs <- c("devtools","dplyr","data.table","MatrixEQTL",
+                 "mvtnorm","reshape2","magrittr","reticulate")
+  to_install <- cran_pkgs[!cran_pkgs %in% rownames(installed.packages())]
+  if (length(to_install)) {
+    msg <- paste("Installing missing CRAN packages:", paste(to_install, collapse = ", "))
+    if (!ask || utils::menu(c("Yes","No"), title = msg) == 1) {
+      install.packages(to_install)
+    }
+  }
+
+  # --- Bioconductor package: qvalue ---
+  if (!requireNamespace("qvalue", quietly = TRUE)) {
+    message("Installing Bioconductor package: qvalue")
+    if (!requireNamespace("BiocManager", quietly = TRUE)) {
+      install.packages("BiocManager")
+    }
+    BiocManager::install("qvalue")
+  }
+
+  # --- Source-only package: TreeQTL ---
+  if (!requireNamespace("TreeQTL", quietly = TRUE)) {
+    message("Installing TreeQTL from source tarball")
+    utils::install.packages("http://bioinformatics.org/treeqtl/TreeQTL_2.0.tar.gz",
+                            repos = NULL, type = "source")
+  }
+
+  # --- Source-only package: TreeBH ---
+  if (!requireNamespace("TreeBH", quietly = TRUE)) {
+    message("Installing TreeBH from source tarball")
+    utils::install.packages("https://github.com/user-attachments/files/21328935/TreeBH_1.0.tar.gz",
+                            repos = NULL, type = "source")
+  }
+
+  message("All FastGxC dependencies are installed or already present.")
+}