--- a
+++ b/R/fetch_online.R
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+#'  Fetch online genome annotations from Ensembldb database
+#'
+#' @param EnsDb_annotations (EndsDb object) - Ensembldb database (default: EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86
+#'
+#' @return gene_range (GRanges object) - Genome annotations
+#' @export
+#'
+#' @examples gene_range = get_genome_annotations(EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86)
+get_genome_annotations <- function(
+  ensdb_annotations = EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86
+  ) {
+  # Get genome annotations from Ensembldb database
+  gene_range <- Signac::GetGRangesFromEnsDb(ensdb_annotations)
+
+  ucsc.levels <- stringr::str_replace(
+    string = paste("chr", Signac::seqlevels(gene_range), sep = ""),
+    pattern = "chrMT",
+    replacement = "chrM") # Change chromosome names to UCSC format
+
+  Signac::seqlevels(gene_range) <- ucsc.levels
+  # check if Signac is the good package
+
+  return(gene_range) # Return genome annotations
+}
+
+#' Fetch online TF motifs from JASPAR2020 and chromVARmotifs
+#'
+#' @param species (character) - Species name (default: "human")
+#'
+#' @return motifs_db (motifs_db object) - TF2motifs + motifs PWMs
+#' @export
+#'
+#' @examples motifs_db = get_tf2motifs(species = "human")
+get_tf2motifs <- function(species = "human") {
+  #TF motifs using the union of databases: JASPAR and cis-BP
+  # included in chromVAR
+  getMatrixSet <- TFBSTools::getMatrixSet
+
+  # If species is human or mouse
+  if (species == "human") {
+    # Parameters for JASPAR2020
+    opts <- list(collection = "CORE",
+              species    = "Homo sapiens",
+              all_versions = FALSE)
+    JASPAR_PWM <- TFBSTools::toPWM(getMatrixSet(JASPAR2020::JASPAR2020, opts))
+    # Load data from JASPAR2020
+    # Load data from chromVARmotifs
+    # Original data accessible at https://github.com/GreenleafLab/chromVARmotifs
+    data("human_pwms_v2")
+    # Load data from chromVARmotifs
+    motifs <- human_pwms_v2
+    # Motifs from chromVARmotifs
+  } else if (species == "mouse") {
+    # Parameters for JASPAR2020
+    opts <- list(collection = "CORE",
+              species    = "Mus musculus",
+              all_versions = FALSE)
+    JASPAR_PWM <- TFBSTools::toPWM(getMatrixSet(JASPAR2020::JASPAR2020, opts))
+    # Load data from JASPAR2020
+    data("mouse_pwms_v2")
+    # Load data from chromVARmotifs
+    # Original data accessible at https://github.com/GreenleafLab/chromVARmotifs
+    motifs <- mouse_pwms_v2
+    # Motifs from chromVARmotifs
+  }
+
+  for (name in names(JASPAR_PWM)){
+    # Combine motifs of JASPAR20202 and chromVARmotif
+    motifs[name] <- JASPAR_PWM[name]
+  }
+
+  # Initiate final TF motifs table
+  tf2motifs <- data.frame(motif = character(),
+                          tf = character(),
+                          stringsAsFactors = FALSE)
+  for (i in seq_along(TFBSTools::name(motifs))){  # Fill TF motif table
+  # TFBSTools::name(motifs) returns names of TFs associated to each PWMatrix
+    tfs <- strsplit(TFBSTools::name(motifs)[i], "::")[[1]]
+    # splitting TFs that are given as "name1::name2"
+    for (tf in tfs){
+      tf <- strsplit(tf, "(", fixed = TRUE)[[1]][1]
+      # only keeping <NAME> in identifier "<NAME>(var.n)"
+      tf2motifs <- rbind(tf2motifs, data.frame(motif = names(motifs)[i],
+                                                             tf = tf))
+    }
+  }
+
+  return(new("motifs_db",
+             tf2motifs = tf2motifs,
+             motifs = motifs,
+             tfs = unique(tf2motifs$tf))) # Return motifs_db <- TF2motifs + motifs PWMs
+}