Export Gene Exploration Data

This function extracts and exports a combined dataset of experimental gene expression data and tKOI network statistics, including key metrics such as log fold changes, p-values, PageRank scores, and adjusted false discovery rates (FDR).

Usage

export_gene_exploration_data(tkoi_list)

Arguments

tkoi_list

An object of class tKOIList. This object must contain the following slots:

• expression_data: A data.frame containing experimental data with columns gene_name, logfc, and pvalue.

• network_summary_statistics: A list with a data.frame for gene-level network statistics, including id, pagerank, beta, p_value, and fdr.

• pvalue_threshold: A numeric value specifying the p-value threshold.

• logfc_threshold: A numeric value specifying the log fold change threshold.

Value

A data.frame with the following columns:

• gene_name: Gene names from the experimental dataset.

• gene_symbol: Gene symbols or common names from the metadata.

• id: Unique node identifiers in the network.

• identifier: External identifiers for the genes (e.g., Ensembl IDs).

• experimental_logfc: Log fold change values from the experimental data.

• experimental_pvalue: P-values from the experimental data.

• pagerank: Personalized PageRank scores from the tKOI network analysis.

• tkoi_beta: tKOI z-scores for network enrichment.

• tkoi_pvalue: Unadjusted p-values from the tKOI network analysis.

• tkoi_fdr: False discovery rates (FDR) from the tKOI network analysis.

Details

The function performs the following steps:

1. Merges the expression_data from the tKOIList object with gene metadata using inner_join.

2. Merges the result with gene-level network data using right_join.

3. Selects key columns from the merged dataset, including:

   • gene_name: Gene names from the experimental data.

   • name: Gene symbols or common names.

   • id and identifier: Unique identifiers for genes in the network.

   • logfc: Experimental log fold change values.

   • pvalue: Experimental p-values.

   • pagerank: tKOI PageRank scores.

   • beta: tKOI z-scores for network enrichment.

   • p_value: tKOI unadjusted p-values.

   • fdr: tKOI false discovery rates (FDR).

4. Renames columns for clarity and standardization.

See also

dplyr, make_gene_exploration_plot

Examples

if (FALSE) { # \dontrun{
# Create a dummy tKOIList object
tkoi_list <- new("tKOIList",
                 expression_data = data.frame(
                   gene_name = c("gene1", "gene2", "gene3"),
                   logfc = c(1.2, -0.8, 0.5),
                   pvalue = c(0.01, 0.03, 0.2)
                 ),
                 network_summary_statistics = list(
                   Gene = data.frame(
                     id = c(1, 2, 3),
                     pagerank = c(0.05, 0.03, 0.02),
                     beta = c(2.1, -1.5, 0.9),
                     p_value = c(0.01, 0.02, 0.05),
                     fdr = c(0.02, 0.03, 0.1)
                   )
                 ),
                 pvalue_threshold = 0.05,
                 logfc_threshold = 0.5)

# Export the gene exploration data
gene_data <- export_gene_exploration_data(tkoi_list)
print(gene_data)
} # }