SearchPathways: Search Pathways in a Given Geneset List

In huayc09/SeuratExtend: SeuratExtend

Search Pathways in a Given Geneset List

Description

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

Usage

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").

Details

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

Value

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

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"))

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.