EnrichmentDFL: Farris et al gene set enrichment data.frames

In jmw86069/farrisdata: Farris et al 2019, mouse hippocampus RNA-seq data objects

Farris et al gene set enrichment data.frames

Description

Farris et al gene set enrichment data.frames

Usage

EnrichmentDFL

Format

list of data.frame objects each with these columns:

• "Comparison" - character string indicating the statistical comparison, and direction of change.

• "P-value" - numeric adjusted enrichment P-value.

• "pathGenes" - integer number of detected genes in each pathway.

• "geneHits" - integer number of gene hits in each pathway.

• "itemsetID" - character identifier for each pathway

• "Source" - character source for each pathway, using MSigDB subcategory where applicable.

• "Name" - short name for each gene set or pathway.

• "Description" - long description for each gene set of pathway.

• "Category" - character string using MSigDB category.

• "geneNames" - character comma-delimited gene symbols including the number of genes in "geneHits".

Details

This object is a list that contains one data.frame for each gene set enrichment test.

Each gene hit list was tested against MSigDB v6.0 using hypergeometric enrichment. The MSigDB data is available from Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Liberzon, et al. (2011, Bionformatics)

Source

Farris et al 2019

Examples

data(EnrichmentDFL);

# show the first few rows of one data.frame
head(EnrichmentDFL[[1]])

# If you have the tibble package, it has a clean display
if (require(tibble)) {
   print(tibble::tibble(EnrichmentDFL[[1]]))
}

# the jamba package sdim() is a good summary
jamba::sdim(EnrichmentDFL);

jmw86069/farrisdata documentation built on Oct. 14, 2024, 6:29 p.m.