get_pathways {genomicper}

Pathways

Description

Helper function to download pathways and their gene identifiers. reactome.db used for pathway annotations.

Usage

get_pathways(source="reactome",all_paths=TRUE,envir = "")

Arguments

source

"reactome"

all_paths

TRUE or FALSE. If FALSE a subset will be asked by the function

envir

R environment to save Pathways to

Value

Returns "Pathways description" All downloaded pathways are saved in the workspace User will be prompt to set a prefix.

See Also

read2_paths

Examples

## Not run: 
# get pathways source = "reactome"
if (!require("reactome.db")) install.packages("reactome.db") 
library(reactome.db)

# Create new environment to save data:
gper.env <- new.env()

paths <- get_pathways(source="reactome",all_paths=FALSE,envir=gper.env)
# when prompted introduce species as listed
Homo sapiens
# when prompted introduce prefix. Avoid characters "-" and "_" (e.g mypath, or leave blank)
# if all_paths set to TRUE. All pathways are downloaded automatically
# IF all_paths set to FALSE, select a subset of pathway identifiers from 
# list. Separated by ","
R-HSA-8964572,R-HSA-9613354,R-HSA-8876384,R-HSA-446343,R-HSA-9620244

## End(Not run)