Pathways

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Description

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

Usage

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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

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## 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)