DEET_example_data {DEET}

DEET_example_data

Description

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.

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.

#'

DEET_DE

A list of data frames containing the significant DE genes, mean expression, log2fold-change, and padj from DESeq (padj < 0.05).

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.

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.

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.

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/'

#'

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/'

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)