pathway_count: Count Genes Present in Pathways Above a Threshold

In TransProR: Analysis and Visualization of Multi-Omics Data

Count Genes Present in Pathways Above a Threshold

Description

This function filters pathways that meet a count threshold and then counts the presence of specified genes in those pathways.

Usage

pathway_count(GO, count_threshold, enrich_data)

Arguments

GO	A character vector of gene symbols.
count_threshold	An integer specifying the count threshold for selecting pathways.
enrich_data	A data frame containing pathway enrichment analysis results.

Value

A data frame with columns "Symble" (gene symbol), "Description" (pathway description), and "Exists" (1 if gene is present, 0 otherwise).

Examples

# Simulated gene list
GO <- c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5")
# Simulated enrichment analysis data
enrich_data <- data.frame(
  ID = c("GO:0001", "GO:0002", "GO:0003"),
  Description = c("Pathway A", "Pathway B", "Pathway C"),
  Count = c(10, 4, 6),
  geneID = c("Gene1/Gene2/Gene3", "Gene4/Gene5", "Gene2/Gene6/Gene7")
)

# Example usage
count_threshold <- 5
result_df <- pathway_count(GO, count_threshold, enrich_data)

TransProR documentation built on April 4, 2025, 3:16 a.m.