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geneontology / panther-enrichment

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
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GO enrichment #20

Open bsmith030465 opened 3 years ago

bsmith030465 commented 3 years ago

This is probably a help question rather than an issue...

I am using R for this script, and the query I execute is:

panther.url <- "http://pantherdb.org/services/oai/pantherdb/enrich/overrep"
pan.body <- list(geneInputList=tgenestr,organism="9606",annotDataSet="GO:0008150") #
myresult <- POST(url=panther.url, body = pan.body, verbose()) # the default
print(myresult)

However, I get an error:

Response [http://pantherdb.org/services/oai/pantherdb/enrich/overrep]
  Date: 2020-09-16 17:15
  Status: 200
  Content-Type: application/json;charset=UTF-8
  Size: 116 B
{"search": {
    "error": "Error annotation type data set not specified",
    "search_type": "overrepresentation"

How should I specify the annotDataSet in my query string?

many thanks!