From 3ec6bee128dc24267e1bab926e627f287449e6df Mon Sep 17 00:00:00 2001
From: pcastellanoescuder <polcaes@gmail.com>
Date: Wed, 13 Dec 2023 15:56:38 -0500
Subject: [PATCH] add protein function predictions

---
 NAMESPACE                                     |  1 +
 R/tables.R                                    | 24 +++++++++++++++++++
 man/make_cluster_enrichment_table.Rd          |  1 -
 ...make_protein_function_predictions_table.Rd | 21 ++++++++++++++++
 4 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 man/make_protein_function_predictions_table.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 1090583..64e6b06 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -75,6 +75,7 @@ export(make_molecular_features_table)
 export(make_molecule_structure)
 export(make_pathway_table)
 export(make_protein_domain)
+export(make_protein_function_predictions_table)
 export(make_protein_sequence)
 export(make_proteinsize)
 export(make_pubmed)
diff --git a/R/tables.R b/R/tables.R
index 0e59ee0..bba3cb1 100644
--- a/R/tables.R
+++ b/R/tables.R
@@ -290,6 +290,30 @@ make_humananatogram_table <- function(input = list()) {
              message(e)
            })
 }
+
+# CAMPBELL MODEL PREDICTIONS -----------------------------------------------
+#' Predicted Protein Functions
+#'
+#' @param input Expecting a list containing a content variable.
+#' @return Returns a table with the predicted protein functions.
+#'
+#' @importFrom magrittr %>%
+#'
+#' @export
+#' @examples
+#' make_protein_function_predictions_table(input = list(content = 'ROCK1'))
+#' make_protein_function_predictions_table(input = list(content = c('ROCK1', 'ROCK2')))
+make_protein_function_predictions_table <- function(input = list()) {
+  predicted_functions <- get_data_object(object_names = input$content,
+                             dataset_name = "protein_function_predictions",
+                             pivotwider = TRUE) %>%
+    dplyr::mutate(Pval = as.numeric(Pvalue), FDR = as.numeric(AdjPvalue)) %>%
+    dplyr::mutate_if(is.numeric, ~ signif(., digits = 3)) %>%
+    dplyr::select(Query = id, `Predicted Function` = Function, Pval, FDR)
+
+  return(predicted_functions)
+}
+
 ## GET CLUSTER  -----------------------------------------------
 #' Clustering Table
 #'
diff --git a/man/make_cluster_enrichment_table.Rd b/man/make_cluster_enrichment_table.Rd
index ebeed28..c95aa54 100644
--- a/man/make_cluster_enrichment_table.Rd
+++ b/man/make_cluster_enrichment_table.Rd
@@ -17,7 +17,6 @@ This is a table function that takes a gene name and returns a clustering enrichm
 }
 \examples{
 make_cluster_enrichment_table(input = list(type = 'gene', content = 'ROCK1'))
-make_cluster_enrichment_table(input = list(type = 'gene', content = 'ROCK1'), ontology = "MF")
 make_cluster_enrichment_table(input = list(type = 'gene', content = c('ROCK1', 'ROCK2')))
 \dontrun{
 make_cluster_enrichment_table(input = list(type = 'gene', content = 'ROCK1'))
diff --git a/man/make_protein_function_predictions_table.Rd b/man/make_protein_function_predictions_table.Rd
new file mode 100644
index 0000000..0478af7
--- /dev/null
+++ b/man/make_protein_function_predictions_table.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tables.R
+\name{make_protein_function_predictions_table}
+\alias{make_protein_function_predictions_table}
+\title{Predicted Protein Functions}
+\usage{
+make_protein_function_predictions_table(input = list())
+}
+\arguments{
+\item{input}{Expecting a list containing a content variable.}
+}
+\value{
+Returns a table with the predicted protein functions.
+}
+\description{
+Predicted Protein Functions
+}
+\examples{
+make_protein_function_predictions_table(input = list(content = 'ROCK1'))
+make_protein_function_predictions_table(input = list(content = c('ROCK1', 'ROCK2')))
+}