get_paths: Convert gene sets to filtered pathway list

In jackbibby1/SCPA: Single Cell Pathway Analysis

Convert gene sets to filtered pathway list

Description

This function takes one of three inputs:

1. csv file where pathway title is in the first column and subsequent columns contain genes of that pathway

2. A gmt file

3. A tidy formatted list where pathway name is contained in the first column and the genes of that pathway are in the second column

Usage

get_paths(pathway_filepath)

Arguments

pathway_filepath

filepath to csv or gmt file

Value

list of pathways with corresponding genes

Examples

## Not run: 
pathways <- get_paths(
     "Documents/gene_list.csv"
)

## End(Not run)

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.