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Unpack clusterProfiler GO Enrichment Results

enrichgo_unpack_ver3.Rd

Unpacks the results of the ORA and outputs a nested list of Terms with their DEGs statistics. Allows users the option to convert the ensemble IDs from clusterProfiler to their named gene-ids

Usage

enrichgo_unpack_ver3(
  initial_table_list = filtered_results,
  key = ora_output_down$enrichgo_results,
  pval_adj_threshold = 0.001,
  convert = FALSE,
  from_type = "ensembl",
  to_type = "symbol",
  org_db = org.Hs.eg.db,
  ensembl_dataset = "hsapiens_gene_ensembl"
)

Arguments

initial_table_list

A list containing the filtered differential expression results for each cluster or comparison. The tables should contain the gene identifiers and differential expression statistics required to associate DEGs with enriched GO terms.

key

A list of over-representation analysis results generated by clusterProfiler, such as the output from enrichGO.

pval_adj_threshold

Numeric value specifying the adjusted p-value threshold used to filter enriched GO terms. Terms with adjusted p-values above this threshold are excluded from the returned results.

convert

Logical value indicating whether gene identifiers should be converted using gene_id_converter_ver2. If TRUE, identifiers are converted from from_type to to_type. If FALSE, the original gene identifiers are retained.

from_type

Character string specifying the original annotation type of the genes. Supported values include "ensembl", "entrez", and "symbol".

to_type

Character string specifying the desired annotation type of the genes. Supported values include "ensembl", "entrez", and "symbol".

org_db

An organism-specific annotation database used to facilitate gene identifier conversion, such as org.Hs.eg.db for human or org.Mm.eg.db for mouse.

ensembl_dataset

Character string specifying the Ensembl dataset used for annotation. For example, "hsapiens_gene_ensembl" for human genes.

Details

For each clusterProfiler result for each comparison available within, extract the gene_ids, then join them with their edgeR differential expression results

References

Yu G, Wang LG, Han Y, He QY., OMICS May, 2012