Fetch WormMine enrichment results for various scenarios

wormMineEnrichmentPublicList.r

#load InterMineR
library(InterMineR)

# Select WormMine
wormMine <- listMines()["WormMine"]
im <- initInterMine(mine=wormMine) # IMPORTANT: ADD YOUR TOKEN HERE IF THIS IS A LIST YOU SAVE TO YOUR OWN ACCOUNT
                                   # EXAMPLE: im <- initInterMine(mine=wormMine, "YOUR TOKEN") 

# fetch the list of widgets available from WormMine
widgets <- getWidgets(im)

print(widgets) # look at the list of widgets - we want go_enrichment_for_gene

# Run the enrichment
GOEnrichmentResult = doEnrichment(
  im = im,
  genelist = "Genes with no life span phenotype (and RNAi not observed) WS265", # This is a public list on WormMine
  widget = "go_enrichment_for_gene"
)

# Print the results 
GOEnrichmentResult

wormMineEnrichmentWithoutWormMineList.r

#load InterMineR
library(InterMineR)

# Select WormMine
wormMine <- listMines()["WormMine"]
im <- initInterMine(mine=wormMine) # IMPORTANT: ADD YOUR TOKEN HERE IF THIS IS A LIST YOU SAVE TO YOUR OWN ACCOUNT
                                   # EXAMPLE: im <- initInterMine(mine=wormMine, "YOUR TOKEN") 

# fetch the list of widgets available from WormMine
widgets <- getWidgets(im)

print(widgets) # look at the list of widgets - we want go_enrichment_for_gene

# List of gene IDs I want to enrich on: 
myGenes <- c("WBGene00001171","WBGene00001190","WBGene00001202","WBGene00001374")

# Run the enrichment
GOEnrichmentResult = doEnrichment(
  im = im,
  ids = myGenes,
  widget = "go_enrichment_for_gene"
)

# Print the results 
GOEnrichmentResult