compareProfiler - Assistance on how I can modify codes for different states

Question

[tpm]

My question is related to the tutorial from this link (https://yulab-smu.github.io/clusterProfiler-book/chapter11.html#formula-interface-of-comparecluster). From this code below, what needs to be modified in order to add more groups if I have “A”, “B”, “C”, “D”....when I don’t only have "A" and "B" states as like seen in this case.

mydf <- data.frame(Entrez=names(geneList), FC=geneList)
mydf <- mydf[abs(mydf$FC) > 1,]
mydf$group <- "upregulated"
mydf$group[mydf$FC < 0] <- "downregulated"
mydf$othergroup <- "A"
mydf$othergroup[abs(mydf$FC) > 2] <- "B"
formula_res <- compareCluster(Entrez~group+othergroup, data=mydf, fun="enrichKEGG")

My raw data sample may be looking like this:

gene    FC  othergroup
glnD    5.237895088 A
eutC    4.64146896  C
mscM    3.947759653 B
tatA    3.920706166 D
elaB    -3.785411053    D
fliI    3.548765407 A
sapD    -3.388648775    B
ppnP    3.345254427 C
ybhA    -3.190667532    C
ilvE    2.900593133 C
tatE    2.865852846 C
oppC    2.853396894 D
glsA1   -2.672349905    D
rnpA    2.563564924 D
ratB    2.473440589 A
ftsI    2.418999465 A
galP    -2.410974203    A
fpr 2.379620962 B
mntR    2.364759177 B
ygiS    -2.337045006    C
speC    -2.252678046    C
srlA    2.227433038 D
yqcA    2.217127294 D
fldB    2.192615021 A

[sangram_keshari]

From this above data seems like you already have othergroup in your data. That above code tried to add group based on conditions.

The above code will generate a dataframe something like this -

mydf

Entrez  group   othergroup 
gene1   upregulated     A
gene2   downregulated   A
gene3   upregulated     B
gene4   upregulated     B
gene5   downregulated   A

So just create such a dataframe then Its matter of using those group header (group, othergroup) names in the formula.

formula_res <- compareCluster(Entrez~group+othergroup, data=mydf, fun="enrichKEGG")