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b/man/pathway_count.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/PathwayCount.R |
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\name{pathway_count} |
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\alias{pathway_count} |
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\title{Count Genes Present in Pathways Above a Threshold} |
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\usage{ |
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pathway_count(GO, count_threshold, enrich_data) |
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} |
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\arguments{ |
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\item{GO}{A character vector of gene symbols.} |
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\item{count_threshold}{An integer specifying the count threshold for selecting pathways.} |
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\item{enrich_data}{A data frame containing pathway enrichment analysis results.} |
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} |
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\value{ |
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A data frame with columns "Symble" (gene symbol), "Description" (pathway description), and "Exists" (1 if gene is present, 0 otherwise). |
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} |
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\description{ |
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This function filters pathways that meet a count threshold and then counts the presence of specified genes in those pathways. |
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} |
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\examples{ |
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# Simulated gene list |
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GO <- c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5") |
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# Simulated enrichment analysis data |
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enrich_data <- data.frame( |
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ID = c("GO:0001", "GO:0002", "GO:0003"), |
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Description = c("Pathway A", "Pathway B", "Pathway C"), |
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Count = c(10, 4, 6), |
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geneID = c("Gene1/Gene2/Gene3", "Gene4/Gene5", "Gene2/Gene6/Gene7") |
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) |
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# Example usage |
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count_threshold <- 5 |
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result_df <- pathway_count(GO, count_threshold, enrich_data) |
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} |