Task 1: show genesets provided by a user

The following command fetches genesets associated with a given user, test in this case. If not parameter is given, the genesets of the current user is provided.

getUserSetsFromGeMS(user="test")

Task 2: insert new genesets to GeMS

New genesets can be inserted into GeMS, using the GmtList data structure defined in the BioQC package, which is essentially a list of lists, which in turn contains three elements: name, desc, and genes. See example below.

testGmt <- BioQC::GmtList(list(
  list(name="Test gene set 1", 
       desc="Test", genes=c("CXCL13", "TNFRSF1B", "RGS2")),
  list(name="Test gene set 2", desc="Test", 
       genes=c("ACADSB", "AFTPH", "ARL1"))
))
insertGmtListToGeMS(testGmt, geneFormat=0, source="Test", xref="PMID:30397336", user="test")

The return value indicates the insertion was successful.

Now we check the genesets of the user test, we expect to see the two gene sets that we inserted.

getUserSetsFromGeMS(user="test")

Alternative to manual specificiation, GmtList can be constructed by reading a valid GMT file with the function readGmt in BioQC.

Task 3: Remove a geneset

The following example shows how a geneset can be removed

removeFromGeMS(setName=c("Test gene set 1", "Test gene set 2"),
               source="Test", user="test")

Now we check the genesets of the user test, we expect to see the two gene sets that we previously inserted should be gone.

getUserSetsFromGeMS(user="test")

Task 4: Retrieve gene-sets with names

The following example shows how genesest can be retrieved by their names. The example was kindly provided by Martha Serrano.

Warning: As shown in the example above, it is very easy to alter genesets in the database. Therefore always make gene set snapshots, never read live data from the database.

gmt_test1_filename <- "data/test1.gmt"
if (file.exists(gmt_test1_filename)) {
  gmt_test1 <- readGmt(gmt_test1_filename)
} else {
  gmt_test1 <- getSetsWithNamesFromGeMS(c("Plasma_sc", "Bcell_l_Danaher17"))
  writeGmt(gmt_test1, gmt_test1_filename)
}
gmt_test1

A caveat of using this function is that it envokes an API call for each geneset. If you need to extract multiple gene-sets, use getSetsWithPropertyFromGeMS (see below).

Task 5: Retrieve gene-sets with a certain property

The following example shows how genesest can be retrieved by matching properties, in this case all cell-marker gene-sets provided by the BESCA package.

Again, we are using GMT snapshots for reproducibility.

besca_markers_filename <- "data/besca_markers.gmt"
if (file.exists(besca_markers_filename)) {
  besca_markers <- readGmt(besca_markers_filename)
} else {
  besca_markers <- getSetsWithPropertyFromGeMS("meta.geneset", "besca_markers")
  writeGmt(besca_markers, besca_markers_filename)
}
print(besca_markers)