compareProfiler - Assistance on how I can modify codes for different states
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
gseGO for multiple groups
written by Omics data mining
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
So just create such a dataframe then Its matter of using those group header (group, othergroup) names in the formula.