markdownTables: Markdown tables

In acidgenomics/pfgsea: Acid Genomics GSEA

Markdown tables

Description

Markdown tables

Usage

markdownTables(object, ...)

## S4 method for signature 'FgseaList'
markdownTables(object, collection, n = 10L, headerLevel = 3L)

Arguments

object	Object.
collection	character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.
n	integer(1). Number of significant processes to include. Bidirectional; will include n up- and down-regulated processes.
headerLevel	integer(1). Markdown header level.
...	Additional arguments.

Details

Top tables of significantly enriched pathways.

Supports looping across multiple DEG results, and adds a Markdown header for each contrast.

Value

kable. Markdown tables.

Note

Updated 2022-05-24.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
alphaThreshold(object) <- 0.9
collection <- collectionNames(object)[[1L]]
markdownTables(
    object = object,
    collection = collection
)

acidgenomics/pfgsea documentation built on April 5, 2025, 9:18 a.m.