genomicper (version 1.6)

get_pathways: Pathways

Description

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

Usage

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

Arguments

source

"reactome" or "kegg"

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 If reactome is selected as the source a prefix will be prompt to be set by user. When kegg is selected the organism identifier is set automatically as the prefix (e.g."hsa").

See Also

read2_paths

Examples

## Not run: 
# # get pathways source = "kegg"
# ## library(KEGG.db)
# 
# # Create new environment to save data:
# gper.env <- new.env()
# 
# # paths <- get_pathways(source="kegg",all_paths=FALSE,envir = gper.env)
# 	# when prompted introduce species as listed
# #	hsa
# 	# if all_paths set to TRUE. All pathways are downloaded automatically
# 	# if all_paths set to FALSE. Introduce list of pathways separated by ","
# 	#hsa00010,hsa00020,hsa04670,hsa04672,hsa04710,hsa04720,hsa04722,hsa04730
# 	
# 
# # get pathways source = "reactome"
# ## library(reactome.db)
# #paths <- get_pathways(source="reactome",all_paths=FALSE,envir=".GlobalEnv")
# 	# when prompted introduce species as listed
# #	Homo sapiens
# 	# when prompted introduce prefix to be assigned to pathways
# 	#HSA
# 	# 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 ","
# 	1500931,1299503,...
# ## End(Not run)