R/DEET_example_data.R

In DEET: Differential Expression Enrichment Tool

#' DEET_example_data
#'
#' Named list of gene-sets and representative metadata for studies associated with Alizada et al., 2021
#' This example data is the exact same as what is needed to run DEET enrich properly but
#' subsetted to have 13 studies that are enriched by `example_DEET_enrich_input`.
#' This way, the example gives an output at all levels of enrichment and at the correlation level.
#'
#'
#' @rdname DEET_example_data
#' @name DEET_example_data
#'
#' @usage data(DEET_example_data)
#'
#' @format A named list of seven objects containing the data frames summarizing the DEGs from comparisons within DEET,
#' GMT objects of comparisons within DEET for enrichment through ActivePathways, GMT objects for basic pathway and TF enrichment,
#' and a dataframe for the metadata of each study.
#'
#' #' \describe{
#'   \item{DEET_DE}{ A list of data frames containing the significant DE genes, mean expression, log2fold-change, and padj from DESeq (padj < 0.05).}
#'   \item{DEET_gmt_BP}{ A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the pathways that are enriched within that study.}
#'   \item{DEET_gmt_TF}{ A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the TFs that are enriched within that study.}
#'   \item{DEET_gmt_DE}{ A list of class GMT, which is a list of studies where each study is populated by comparison id (internal DEET identifier), comparison name (interpretable comparison name), and a gene set. In this case the gene-set is the DEGs that are enriched within that study.}
#'   \item{gmt_BP}{ A list of class GMT, which is a list of gene ontology gene-sets acquired from the bader lab `http://download.baderlab.org/EM_Genesets/`}#'
#'   \item{gmt_TF}{ A list of class GMT, which is a list of Transcription Factor gene-sets acquired from the bader lab `http://download.baderlab.org/EM_Genesets/`}
#'   \item{DEET_metadata}{ For every pairwise comparison, the study name, source (SRA, TCGA, GTEx and SRA-manual), description from the DRA compendium, the number of samples (total, up-condition, and down-condition), samples (total ,up-condition, down-condition), tissue (including tumour from TCGA), number of DEs (total, up-condition, down-condition), age (mean +- sd), sex, top 15 DEGs - up, top 15 DEGs - down, top 5 enriched pathways, and top 5 enriched TFs. PMID are also available for studies selected from SRA. Lastly, each pairwise comparison was given an overall category based on those decided in Crow et al., 2019. }
#' }
#'
#' @examples
#' data(DEET_example_data)
#' @keywords datasets
#'
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