Contents

Citation: if you use MAGeCKFlute in published research, please cite: Binbin Wang, Mei Wang, Wubing Zhang. “Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.” Nature Protocols (2019), doi: 10.1038/s41596-018-0113-7.t

1 Input data - weighted gene list

library(MAGeCKFlute)
file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
                  "testdata/rra.gene_summary.txt")
gdata = ReadRRA(file1)
genelist = gdata$Score
names(genelist) = gdata$id
genelist[1:5]
##   CREBBP    EP300      CHD C16orf72   CACNB2 
##  0.96608  1.02780  0.59265  0.82307  0.39268

2 Enrichment analysis methods

MAGeCKFlute incorporates three enrichment methods, including Over-Representation Test (ORT), Gene Set Enrichment Analysis (GSEA), and Hypergeometric test (HGT). Here, ORT and GSEA are borrowed from R package clusterProfiler (Yu et al. 2012).

2.1 Hypergeometric test

# Alternative functions EnrichAnalyzer and enrich.HGT.
hgtRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "HGT")
head(hgtRes1@result)
##                                                                                                                  ID
## REACTOME_2467813                                                                                   REACTOME_2467813
## REACTOME_72163                                                                                       REACTOME_72163
## GO_TRNA_METABOLIC_PROCESS                                                                 GO_TRNA_METABOLIC_PROCESS
## GO_SISTER_CHROMATID_SEGREGATION                                                     GO_SISTER_CHROMATID_SEGREGATION
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS
## REACTOME_68949                                                                                       REACTOME_68949
##                                                                                                      Description
## REACTOME_2467813                                                                 Separation of Sister Chromatids
## REACTOME_72163                                                                     mRNA Splicing - Major Pathway
## GO_TRNA_METABOLIC_PROCESS                                                                 TRNA METABOLIC PROCESS
## GO_SISTER_CHROMATID_SEGREGATION                                                     SISTER CHROMATID SEGREGATION
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS
## REACTOME_68949                                                                       Orc1 removal from chromatin
##                                                                  NES
## REACTOME_2467813                                          -10.350541
## REACTOME_72163                                            -10.123151
## GO_TRNA_METABOLIC_PROCESS                                 -10.970698
## GO_SISTER_CHROMATID_SEGREGATION                            -9.637773
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS  -7.591227
## REACTOME_68949                                             -7.619360
##                                                                 pvalue
## REACTOME_2467813                                          5.258300e-14
## REACTOME_72163                                            1.844729e-13
## GO_TRNA_METABOLIC_PROCESS                                 8.226663e-13
## GO_SISTER_CHROMATID_SEGREGATION                           2.943300e-12
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS 4.637988e-11
## REACTOME_68949                                            8.565588e-11
##                                                               p.adjust
## REACTOME_2467813                                          4.306548e-11
## REACTOME_72163                                            7.554166e-11
## GO_TRNA_METABOLIC_PROCESS                                 2.245879e-10
## GO_SISTER_CHROMATID_SEGREGATION                           6.026407e-10
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS 7.597025e-09
## REACTOME_68949                                            1.069499e-08
##                                                           GeneRatio BgRatio
## REACTOME_2467813                                             24/190 190/190
## REACTOME_72163                                               23/183 183/183
## GO_TRNA_METABOLIC_PROCESS                                    22/178 178/178
## GO_SISTER_CHROMATID_SEGREGATION                              22/189 189/189
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS     14/81   81/81
## REACTOME_68949                                                13/71   71/71
##                                                                                                                                                                                       geneID
## REACTOME_2467813                                          29945/5708/54820/5689/5695/5518/701/25936/5688/8697/81930/5702/5692/5347/10403/5691/147841/9212/100527963/5885/1778/8243/5686/9184
## REACTOME_72163                                                6426/1479/56949/5435/6632/27339/23398/7536/54883/29894/5433/51340/10523/8175/10262/9775/1660/1665/3192/25804/10772/23020/23517
## GO_TRNA_METABOLIC_PROCESS                                  79897/4677/51637/285381/1615/8565/57505/51520/60528/51367/29894/90353/10056/283989/3035/112858/51067/7407/348180/54938/3028/55226
## GO_SISTER_CHROMATID_SEGREGATION                                      29945/79643/79075/5518/701/25936/8697/81930/55294/23397/5347/10403/11331/9212/7153/5885/79892/27243/8243/3192/9184/3837
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS                                                              29945/5708/5689/5695/701/5688/8697/5702/5692/5347/5691/9212/5686/9184
## REACTOME_68949                                                                                                              5708/5689/5695/5688/4175/5702/5692/5691/4171/890/9978/5686/23594
##                                                                                                                                                                                                   geneName
## REACTOME_2467813                                           ANAPC4/PSMD2/NDE/PSMB1/PSMB7/PPP2R1A/BUB1B/NSL1/PSMA7/CDC23/KIF18A/PSMC3/PSMB4/PLK1/NDC80/PSMB3/SPC24/AURKB/PMF1/RAD21/DYNC1H1/SMC1A/PSMA5/BUB3
## REACTOME_72163                                            SRSF1/CSTF3/XAB2/POLR2F/SNRPD/PRPF19/PPWD1/SF1/CWC25/CPSF1/POLR2D/CRNKL1/CHERP/SF3A2/SF3B4/EIF4A3/DHX9/DHX15/HNRNPU/LSM4/SRSF10/SNRNP200/SKIV2L2
## GO_TRNA_METABOLIC_PROCESS                                                 RPP21/NARS/C14orf166/DPH3/DARS/YARS/AARS2/LARS/ELAC2/POP5/CPSF1/CTU1/FARSB/TSEN54/HARS/TP53RK/YARS2/VARS/CTU2/SYS/HSD17B10/NAT10
## GO_SISTER_CHROMATID_SEGREGATION                                       ANAPC4/CHMP6/DSCC1/PPP2R1A/BUB1B/NSL1/CDC23/KIF18A/CDC4/NCAPH/PLK1/NDC80/PHB2/AURKB/TOP2A/RAD21/MCMBP/CHMP2A/SMC1A/HNRNPU/BUB3/KPNB1
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS                                                               ANAPC4/PSMD2/PSMB1/PSMB7/BUB1B/PSMA7/CDC23/PSMC3/PSMB4/PLK1/PSMB3/AURKB/PSMA5/BUB3
## REACTOME_68949                                                                                                                   PSMD2/PSMB1/PSMB7/PSMA7/MCM6/PSMC3/PSMB4/PSMB3/MCM2/CCNA2/RBX1/PSMA5/ORC6
##                                                           Count
## REACTOME_2467813                                             24
## REACTOME_72163                                               23
## GO_TRNA_METABOLIC_PROCESS                                    22
## GO_SISTER_CHROMATID_SEGREGATION                              22
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS    14
## REACTOME_68949                                               13
# hgtRes2 = enrich.HGT(genelist[genelist< -1])
# head(hgtRes2@result)

2.2 Over-representation test

# Alternative functions EnrichAnalyzer and enrich.ORT.
ortRes1 = EnrichAnalyzer(genelist[genelist< -1], method = "ORT")
head(ortRes1@result)
##                                                                                                                  ID
## REACTOME_2467813                                                                                   REACTOME_2467813
## REACTOME_72163                                                                                       REACTOME_72163
## GO_TRNA_METABOLIC_PROCESS                                                                 GO_TRNA_METABOLIC_PROCESS
## GO_SISTER_CHROMATID_SEGREGATION                                                     GO_SISTER_CHROMATID_SEGREGATION
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS
## GO_RNA_3_END_PROCESSING                                                                     GO_RNA_3_END_PROCESSING
##                                                                                                      Description
## REACTOME_2467813                                                                 Separation of Sister Chromatids
## REACTOME_72163                                                                     mRNA Splicing - Major Pathway
## GO_TRNA_METABOLIC_PROCESS                                                                 TRNA METABOLIC PROCESS
## GO_SISTER_CHROMATID_SEGREGATION                                                     SISTER CHROMATID SEGREGATION
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS ANAPHASE PROMOTING COMPLEX DEPENDENT CATABOLIC PROCESS
## GO_RNA_3_END_PROCESSING                                                                     RNA 3 END PROCESSING
##                                                                  NES
## REACTOME_2467813                                          -10.350541
## REACTOME_72163                                            -10.123151
## GO_TRNA_METABOLIC_PROCESS                                 -10.970698
## GO_SISTER_CHROMATID_SEGREGATION                            -9.637773
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS  -7.591227
## GO_RNA_3_END_PROCESSING                                    -8.926127
##                                                                 pvalue
## REACTOME_2467813                                          1.542034e-13
## REACTOME_72163                                            5.619434e-13
## GO_TRNA_METABOLIC_PROCESS                                 2.572894e-12
## GO_SISTER_CHROMATID_SEGREGATION                           8.679735e-12
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS 2.956773e-10
## GO_RNA_3_END_PROCESSING                                   3.467555e-10
##                                                               p.adjust
## REACTOME_2467813                                          4.259099e-10
## REACTOME_72163                                            7.760439e-10
## GO_TRNA_METABOLIC_PROCESS                                 2.368777e-09
## GO_SISTER_CHROMATID_SEGREGATION                           5.993357e-09
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS 1.596231e-07
## GO_RNA_3_END_PROCESSING                                   1.596231e-07
##                                                           GeneRatio   BgRatio
## REACTOME_2467813                                             24/288 190/15323
## REACTOME_72163                                               23/288 183/15323
## GO_TRNA_METABOLIC_PROCESS                                    22/288 178/15323
## GO_SISTER_CHROMATID_SEGREGATION                              22/288 189/15323
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS    14/288  81/15323
## GO_RNA_3_END_PROCESSING                                      18/288 148/15323
##                                                                                                                                                                                       geneID
## REACTOME_2467813                                          29945/5708/54820/5689/5695/5518/701/25936/5688/8697/81930/5702/5692/5347/10403/5691/147841/9212/100527963/5885/1778/8243/5686/9184
## REACTOME_72163                                                6426/1479/56949/5435/6632/27339/23398/7536/54883/29894/5433/51340/10523/8175/10262/9775/1660/1665/3192/25804/10772/23020/23517
## GO_TRNA_METABOLIC_PROCESS                                  79897/4677/51637/285381/1615/8565/57505/51520/60528/51367/29894/90353/10056/283989/3035/112858/51067/7407/348180/54938/3028/55226
## GO_SISTER_CHROMATID_SEGREGATION                                      29945/79643/79075/5518/701/25936/8697/81930/55294/23397/5347/10403/11331/9212/7153/5885/79892/27243/8243/3192/9184/3837
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS                                                              29945/5708/5689/5695/701/5688/8697/5702/5692/5347/5691/9212/5686/9184
## GO_RNA_3_END_PROCESSING                                                                580/64852/6426/170506/1479/2091/60528/9984/114034/80145/29894/5433/55656/56915/54512/9775/134353/3028
##                                                                                                                                                                                                    geneName
## REACTOME_2467813                                          ANAPC4/PSMD2/NDE1/PSMB1/PSMB7/PPP2R1A/BUB1B/NSL1/PSMA7/CDC23/KIF18A/PSMC3/PSMB4/PLK1/NDC80/PSMB3/SPC24/AURKB/PMF-1/RAD21/DYNC1H1/SMC1A/PSMA5/BUB3
## REACTOME_72163                                              SRSF1/CSTF3/XAB2/POLR2F/SNRPD1/PRPF19/PPWD1/SF1/CWC25/CPSF1/POLR2D/CRNKL1/CHERP/SF3A2/SF3B4/EIF4A3/DHX9/DHX15/HNRNPU/LSM4/SRSF10/SNRNP200/MTREX
## GO_TRNA_METABOLIC_PROCESS                                              RPP21/NARS1/RTRAF/DPH3/DARS1/YARS1/AARS2/LARS1/ELAC2/POP5/CPSF1/CTU1/FARSB/TSEN54/HARS1/TP53RK/YARS2/VARS1/CTU2/SARS2/HSD17B10/NAT10
## GO_SISTER_CHROMATID_SEGREGATION                                       ANAPC4/CHMP6/DSCC1/PPP2R1A/BUB1B/NSL1/CDC23/KIF18A/FBXW7/NCAPH/PLK1/NDC80/PHB2/AURKB/TOP2A/RAD21/MCMBP/CHMP2A/SMC1A/HNRNPU/BUB3/KPNB1
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS                                                                ANAPC4/PSMD2/PSMB1/PSMB7/BUB1B/PSMA7/CDC23/PSMC3/PSMB4/PLK1/PSMB3/AURKB/PSMA5/BUB3
## GO_RNA_3_END_PROCESSING                                                                     BARD1/PAPD2/SRSF1/DHX36/CSTF3/FBL/ELAC2/THOC1/TOE1/THOC7/CPSF1/POLR2D/INTS8/EXOSC5/EXOSC4/EIF4A3/LSM11/HSD17B10
##                                                           Count
## REACTOME_2467813                                             24
## REACTOME_72163                                               23
## GO_TRNA_METABOLIC_PROCESS                                    22
## GO_SISTER_CHROMATID_SEGREGATION                              22
## GO_ANAPHASE_PROMOTING_COMPLEX_DEPENDENT_CATABOLIC_PROCESS    14
## GO_RNA_3_END_PROCESSING                                      18
# ortRes2 = enrich.ORT(genelist[genelist< -1])
# head(ortRes2@result)

2.3 Gene set enrichment analysis

# Alternative functions EnrichAnalyzer and enrich.GSE.
gseRes1 = EnrichAnalyzer(genelist, method = "GSEA")
## Warning in .GSEA(geneList = geneList, exponent = exponent, minGSSize =
## minGSSize, : We do not recommend using nPerm parameter incurrent and future
## releases
## Warning in fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize
## = minGSSize, : You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (2.56% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
head(gseRes1@result)
##                                                                                                                    ID
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                               GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                                             GO_CELLULAR_KETONE_METABOLIC_PROCESS
## GO_PROTEIN_ACETYLATION                                                                         GO_PROTEIN_ACETYLATION
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN   GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR
## REACTOME_2467813                                                                                     REACTOME_2467813
##                                                                                                        Description
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                               REGULATION OF LIPID BIOSYNTHETIC PROCESS
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                                             CELLULAR KETONE METABOLIC PROCESS
## GO_PROTEIN_ACETYLATION                                                                         PROTEIN ACETYLATION
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN   ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR REGULATION OF SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR
## REACTOME_2467813                                                                   Separation of Sister Chromatids
##                                                                  NES
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                -1.693697
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                       -1.705535
## GO_PROTEIN_ACETYLATION                                     -1.712543
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN  -1.914588
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR -1.693346
## REACTOME_2467813                                           -2.318692
##                                                                  pvalue
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                0.0005246590
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                       0.0005254861
## GO_PROTEIN_ACETYLATION                                     0.0005260389
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN  0.0005274262
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR 0.0005274262
## REACTOME_2467813                                           0.0005299417
##                                                              p.adjust
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                0.03139187
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                       0.03139187
## GO_PROTEIN_ACETYLATION                                     0.03139187
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN  0.03139187
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR 0.03139187
## REACTOME_2467813                                           0.03139187
##                                                                                                                                                                                                                                                                                                             geneID
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                                                                                                                                                                           4802/4800/51085/672/6309/11218/6713/2222/6647/2194/10654/3837/10399/4047/2475/7536/3157/3692
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                                                                                                                                                          5693/133/84274/6770/5707/2739/5719/5709/10197/5690/9861/51805/7167/5702/5686/5692/5695/5708/5688/2821/2475/5689/5691
## GO_PROTEIN_ACETYLATION                                                                                                                                                              54386/339287/2648/117143/6877/51616/10847/8260/54934/672/64769/8089/8607/80155/2959/84148/79075/86/80018/1111/3054/122830/6880
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN                                                                                                           10120/5707/10437/5719/5709/6396/10197/1062/3796/10671/51164/84516/5690/11004/9861/11258/829/5702/5686/81930/1778/5692/5695/5708/5688/5689/5691
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR                                                                                             10524/1655/83990/79915/1263/23246/80279/960/6874/9219/83695/6877/51616/672/5982/64769/6749/22974/112858/6118/5810/23028/4839/55702/9212/83860/1111/580/6880
## REACTOME_2467813                                           5719/23244/9735/11130/54821/55746/5709/79019/6396/23047/10197/1062/1063/57405/3796/113130/10274/5690/11004/9861/5905/701/5518/5702/8697/54820/9184/5686/81930/5885/29945/1778/5692/5695/5708/147841/25936/5688/8243/9212/10403/5689/5347/100527963/5691
##                                                                                                                                                                                                                                                                                                                                        geneName
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                                                                                                                                                                                                    NFYC/NFYA/MLXIPL/BRCA1/SC5D/DDX20/SQLE/FDFT1/SOD1/FASN/PMVK/KPNB1/RACK1/LSS/MTOR/SF1/HMGCS1/EIF6
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                                                                                                                                                                           PSMB5/ADM/COQ5/STAR/PSMD1/GLO1/PSMD13/PSMD3/PSME3/PSMB2/PSMD6/COQ3/TPI1/PSMC3/PSMA5/PSMB4/PSMB7/PSMD2/PSMA7/GPI/MTOR/PSMB1/PSMB3
## GO_PROTEIN_ACETYLATION                                                                                                                                                                              TERF2IP/MSL1/KAT2A/TADA1/TAF5/TAF9B/SRCAP/NAA10/KANSL2/BRCA1/MEAF6/YEATS4/RUVBL1/NAA15/GTF2B/KAT8/DSCC1/ACTL6A/NAA25/CHEK1/HCFC1/NAA30/TAF9
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN                                                                                                               ACTR1B/PSMD1/IFI30/PSMD13/PSMD3/SEC13/PSME3/CENPE/KIF2A/DCTN6/DCTN4/DCTN5/PSMB2/KIF2C/PSMD6/DCTN3/CAPZA1/PSMC3/PSMA5/KIF18A/DYNC1H1/PSMB4/PSMB7/PSMD2/PSMA7/PSMB1/PSMB3
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR                                                                                                                    KAT5/DDX5/BRIP1/ATAD5/PLK3/BOP1/CDK5RAP3/CD44/TAF4/MTA2/RHNO1/TAF5/TAF9B/BRCA1/RFC2/MEAF6/SSRP1/TPX2/TP53RK/RPA2/RAD1/KDM1A/NOP2/YJU2/AURKB/TAF3/CHEK1/BARD1/TAF9
## REACTOME_2467813                                           PSMD13/PDS5A/KNTC1/ZWINT/ERCC6L/NUP133/PSMD3/CENPM/SEC13/PDS5B/PSME3/CENPE/CENPF/SPC25/KIF2A/CDCA5/STAG1/PSMB2/KIF2C/PSMD6/RANGAP1/BUB1B/PPP2R1A/PSMC3/CDC23/NDE1/BUB3/PSMA5/KIF18A/RAD21/ANAPC4/DYNC1H1/PSMB4/PSMB7/PSMD2/SPC24/NSL1/PSMA7/SMC1A/AURKB/NDC80/PSMB1/PLK1/PMF-1/PSMB3
##                                                            Count
## GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS                   18
## GO_CELLULAR_KETONE_METABOLIC_PROCESS                          23
## GO_PROTEIN_ACETYLATION                                        23
## GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_PEPTIDE_ANTIGEN     27
## GO_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR    29
## REACTOME_2467813                                              45
# gseRes2 = enrich.GSE(genelist)
# head(gseRes2@result)

2.4 Visualize enrichment results.

2.4.1 Barplot

require(ggplot2)
df = hgtRes1@result
df$logFDR = -log10(df$p.adjust)
p = BarView(df[1:5,], "Description", 'logFDR')
p = p + labs(x = NULL) + coord_flip()
p

# Or use function barplot from enrichplot package
barplot(hgtRes1, showCategory = 5)

2.4.2 Dot plot

EnrichedView(hgtRes1, bottom = 5, mode = 1)

EnrichedView(hgtRes1, bottom = 5, mode = 2)