Process the enrichment results from Enrichr

Process the enrichment results from Enrichr

Usage

prepare_enrichr_result(data, dbname = "Database", n_input = NULL)

Arguments

data

A data frame containing the result by Enrichr.

dbname

A character string specifying the name of the database column.

n_input

An integer specifying the number of input genes. Enrichr result doesn't ship with the number of input genes. You can either provide the number directly or we will infer it. See details.

Value

A data frame that can be used in EnrichMap.

Details

In order to use the EnrichMap and EnrichNetwork functions and other visualization functions in plotthis, the enrichment results from Enrichr need to be processed by the prepare_enrichr_result function. The following columns are renamed:

• Term -> Description

• Genes -> geneID (separated replaced by /)

• P.value -> pvalue

• Adjusted.P.value -> p.adjust Additionally, GeneRatio and BgRatio columns are inferred. From enrichr's documentation, the oddsRatio is defined as: oddsRatio = (A * (D - B - C + A) / max((B - A) * (C - A), 1), where A is the overlapping genes; B is the total genes in the gene set; C (n_input) is the genes in input list; D is the total genes in the background. D is not provided by Enrichr. To infer it, D = oddsRatio * max((B - A) * (C - A), 1) / A + B + C - A.

• Overlap = A / B (from Enrichr)

• GeneRatio = A / C (from ClusterProfiler)

• BgRatio = B / D (from ClusterProfiler) C (n_input), if not provided, will be inferred when D for all terms are equal. When starting inferrence, the minimum value to try will be unique genes in data$Genes/data$geneID.