| DEET_enrich {DEET} | R Documentation |
DEET_enrich
Description
Core function of DEET where an input weighted human gene list will be queried to DEETs library of studies.
Usage
DEET_enrich(
DEG_list,
DEET_dataset,
ordered = FALSE,
background = NULL,
abs_cor = FALSE
)
Arguments
DEG_list |
Data frame or matrix of gene symbols with corresponding padj and log2FC values (3 columns in total). Can also be a character vector of gene symbols only. colnames of genes: c("gene_symbol", "padj", "coef") The rownames of the dataframe are also the gene symbols. |
DEET_dataset |
The databank of the differential expression enrichment tool. Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y. The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data. |
ordered |
Boolean value specifying whether DEG_list is a character vector of gene symbols that is ordered. Default value is FALSE. |
background |
Character vector of human gene symbols showing all possible genes. Default value is NULL. |
abs_cor |
Boolean value that forces log2FC's in DEET to be their absolute value. Use when the directionality of the coefficient is unknown (or includes both up- down- directions). Default value is FALSE. |
Value
Named list where each element contains 6 objects. Each object will contain the results (enrichment or correlation) and corresponding metadata.
AP_INPUT_BP_output - Enriched BPs of input gene list.
AP_INPUT_TF_output - Enriched TFs of input gene list.
AP_DEET_DE_output - Enrichment of input gene list on DEETs studies.
AP_DEET_BP_output - Enrichment of BPs of input gene list on DEETs BPs of studies.
AP_DEET_TF_output - Enrichment of TFs of input gene list on DEETs TFs of studies.
DE_correlations - Correlation values of input gene list to DEETs studies (both Pearson and Spearman).
Author(s)
Dustin Sokolowski, Jedid Ahn
References
Paczkowska M, Barenboim J, Sintupisut N, et al. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020;11(1):735. doi:10.1038/s41467-019-13983-9
Examples
data("example_DEET_enrich_input")
data("DEET_example_data")
DEET_out <- DEET_enrich(example_DEET_enrich_input, DEET_dataset = DEET_example_data)