Search Pathways in a Given Geneset List

This function filters a provided geneset list based on a specified gene name, or pathway name.

SearchPathways(genesets, item, type = c("gene", "SetName"))

Arguments

genesets

A list of genesets where the names are pathway names and the contents are genes.

item

A vector containing gene names or (parts of) pathway names to search for.

type

Specifies the types of search criteria. This can be "gene", "SetName", or both. Default is c("gene", "SetName").

Value

A subset of the provided geneset list containing the specified items.

Details

For more details and use-cases, see the examples section.

Examples

library(SeuratExtend)
library(dplyr)
options(max.print = 10)

# Check within the hallmark 50 database for pathways that contain the "CD3D" gene
# or have pathway names that include "interferon".
SearchPathways(genesets = hall50$human, item = c("CD3D", "interferon"))