I'm doing GO enrichment analysis using clusterProfiler. I used minGSSize filter (10, seems like it's default though) to restrict gene size, but I got enrichment terms with less than 10 elements.
I can manually filter them out. But, I'm concerning whether it is a proper way of handling this, and whether I get wrong statistical numbers (pvalue etc.) because of filtering failure or something. I have more cases but posted one case with example code below.
require(clusterProfiler)
require(org.At.tair.db)
# sorry for this annoying input list, but my original input list is longer than this.
GOI <- c("AT1G02920", "AT1G02930", "AT1G03620", "AT1G03760", "AT1G03880", "AT1G05675", "AT1G11610", "AT1G12790", "AT1G13520", "AT1G13990", "AT1G14540", "AT1G14950", "AT1G15125", "AT1G15670", "AT1G15920", "AT1G16030", "AT1G19250", "AT1G21110", "AT1G21120", "AT1G24100", "AT1G24330", "AT1G26250", "AT1G26380", "AT1G26390", "AT1G26410", "AT1G26420", "AT1G27565", "AT1G44130", "AT1G47540", "AT1G49000", "AT1G51920", "AT1G53950", "AT1G56240", "AT1G56250", "AT1G61970", "AT1G62130", "AT1G63860", "AT1G64400", "AT1G65486", "AT1G65845", "AT1G66500", "AT1G66700", "AT1G66920", "AT1G67270", "AT1G68230", "AT1G68862", "AT1G69280", "AT1G69920", "AT1G69930", "AT1G70140", "AT1G72060", "AT1G72900", "AT1G74360", "AT1G74590", "AT1G75000", "AT1G75335", "AT1G75830", "AT1G80840", "AT2G02010", "AT2G02930", "AT2G07698", "AT2G07719", "AT2G15220", "AT2G17040", "AT2G18370", "AT2G18660", "AT2G19910", "AT2G24600", "AT2G25470", "AT2G27389", "AT2G28450", "AT2G29330", "AT2G32190", "AT2G32830", "AT2G33580", "AT2G35980", "AT2G36950", "AT2G38860", "AT2G38870", "AT2G39210", "AT2G39350", "AT2G39400", "AT2G41010", "AT2G41280", "AT2G43000", "AT2G44370", "AT2G46430", "AT2G46650", "AT3G09405", "AT3G15340", "AT3G15518", "AT3G15590", "AT3G16020", "AT3G16030", "AT3G16530", "AT3G19470", "AT3G22800", "AT3G23150", "AT3G23250", "AT3G23570", "AT3G25900", "AT3G26170", "AT3G26210", "AT3G26830", "AT3G27870", "AT3G29100", "AT3G45420", "AT3G51450", "AT3G53160", "AT3G54150", "AT3G58930", "AT4G01010", "AT4G02280", "AT4G02520")
enrichGO_test <-
enrichGO(GOI,
maxGSSize = 500,
minGSSize = 10,
OrgDb = org.At.tair.db,
ont = 'BP',
keyType = 'TAIR',
pvalueCutoff = 0.01,
pAdjustMethod = 'BH',
qvalueCutoff = 0.01
)
# plot image view
dotplot(enrichGO_test)
# table view
View(enrichGO_test@result)
enrichGO_test@result[enrichGO_test@result$ID == 'GO:0071456',]
In the dotplot(enrichGO_test) result above, GO(GO:0071456) with description 'cellular response to hypoxia' plotted, but GeneRatio for the term has '4/88'.
Versions:
R version 3.6.1 (2019-07-05) clusterProfiler version 3.12.0 RStudio 1,2,1335 Bioconductor version 3.9 (BiocManager 1.30.8)
The minGSSize and maxGSSize are used to restrict gene set size not for your gene list. If we looking at the formula, https://yulab-smu.github.io/clusterProfiler-book/chapter2.html#over-representation-analysis, they apply to the M.
Thank you for correcting me. What I had mentioned above seems to be the 'k' then, and what I wanted in the original question seems like the gsfilter() function as in the link below. https://github.com/YuLab-SMU/clusterProfiler/issues/46
So, I can filter my result as follows.
enrichGO_test_filter10 <- gsfilter(enrichGO_test, by = 'Count', min = 10)
View(enrichGO_test_filter10@result)
Looks great! Thanks again.
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