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+++ b/man/gene_map_pathway.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/GeneMapPathway.R
+\name{gene_map_pathway}
+\alias{gene_map_pathway}
+\title{Create Pathway-Gene Mapping Data Frame}
+\usage{
+gene_map_pathway(
+  BP_dataframe,
+  BP_ids,
+  KEGG_dataframe,
+  KEGG_ids,
+  MF_dataframe,
+  MF_ids,
+  REACTOME_dataframe,
+  REACTOME_ids,
+  CC_dataframe,
+  CC_ids,
+  DO_dataframe,
+  DO_ids
+)
+}
+\arguments{
+\item{BP_dataframe}{Data frame for Biological Process analysis}
+
+\item{BP_ids}{Selected pathway IDs for Biological Process analysis}
+
+\item{KEGG_dataframe}{Data frame for KEGG analysis}
+
+\item{KEGG_ids}{Selected pathway IDs for KEGG analysis}
+
+\item{MF_dataframe}{Data frame for Molecular Function analysis}
+
+\item{MF_ids}{Selected pathway IDs for Molecular Function analysis}
+
+\item{REACTOME_dataframe}{Data frame for REACTOME analysis}
+
+\item{REACTOME_ids}{Selected pathway IDs for REACTOME analysis}
+
+\item{CC_dataframe}{Data frame for Cellular Component analysis}
+
+\item{CC_ids}{Selected pathway IDs for Cellular Component analysis}
+
+\item{DO_dataframe}{Data frame for Disease Ontology analysis}
+
+\item{DO_ids}{Selected pathway IDs for Disease Ontology analysis}
+}
+\value{
+A new data frame that includes pathways, gene, type, and value columns
+}
+\description{
+This function takes multiple data frames and pathway IDs, merging them into a new data frame.
+Each data frame represents a type of analysis (e.g., BP, KEGG, MF, etc.).
+}
+\examples{
+# Simulating data for different analysis types
+
+# Simulate Biological Process (BP) data frame
+BP_df <- data.frame(
+  ID = c("GO:0002376", "GO:0019724"),
+  geneID = c("GENE1/GENE2", "GENE3/GENE4"),
+  Description = c("Immune response", "Glycosylation process")
+)
+
+# Simulate KEGG data frame
+KEGG_df <- data.frame(
+  ID = c("12345", "67890"),
+  geneID = c("GENE5/GENE6", "GENE7/GENE8"),
+  Description = c("Pathway 1", "Pathway 2")
+)
+
+# Simulate Molecular Function (MF) data frame
+MF_df <- data.frame(
+  ID = c("ABC123", "DEF456"),
+  geneID = c("GENE9/GENE10", "GENE11/GENE12"),
+  Description = c("Molecular function A", "Molecular function B")
+)
+
+# Simulate REACTOME data frame
+REACTOME_df <- data.frame(
+  ID = c("R-HSA-12345", "R-HSA-67890"),
+  geneID = c("GENE13/GENE14", "GENE15/GENE16"),
+  Description = c("Pathway in Reactome 1", "Pathway in Reactome 2")
+)
+
+# Simulate Cellular Component (CC) data frame
+CC_df <- data.frame(
+  ID = c("GO:0005575", "GO:0005634"),
+  geneID = c("GENE17/GENE18", "GENE19/GENE20"),
+  Description = c("Cellular component A", "Cellular component B")
+)
+
+# Simulate Disease Ontology (DO) data frame
+DO_df <- data.frame(
+  ID = c("DOID:123", "DOID:456"),
+  geneID = c("GENE21/GENE22", "GENE23/GENE24"),
+  Description = c("Disease A", "Disease B")
+)
+
+# Example pathway IDs for each analysis
+BP_ids <- c("GO:0002376", "GO:0019724")
+KEGG_ids <- c("12345", "67890")
+MF_ids <- c("ABC123", "DEF456")
+REACTOME_ids <- c("R-HSA-12345", "R-HSA-67890")
+CC_ids <- c("GO:0005575", "GO:0005634")
+DO_ids <- c("DOID:123", "DOID:456")
+
+# Generate the pathway-gene map using the gene_map_pathway function
+pathway_gene_map <- gene_map_pathway(
+  BP_dataframe = BP_df, BP_ids = BP_ids,
+  KEGG_dataframe = KEGG_df, KEGG_ids = KEGG_ids,
+  MF_dataframe = MF_df, MF_ids = MF_ids,
+  REACTOME_dataframe = REACTOME_df, REACTOME_ids = REACTOME_ids,
+  CC_dataframe = CC_df, CC_ids = CC_ids,
+  DO_dataframe = DO_df, DO_ids = DO_ids
+)
+
+# Display the resulting pathway-gene mapping data frame
+print(pathway_gene_map)
+
+}