The outputs of ORA and GSEA are enrichResult and gseaResult objects, respectively, while the output of compareCluster is a compareClusterResult object. These S4 objects contain input data, analysis settings, and enriched results, which allow more informative data to be available for downstream interpretation and visualization. To enable easy access to the enriched result, clusterProfiler implements as.data.frame methods to convert the S4 objects to data frames that can be easily exported as CSV files. In addition, clusterProfiler provides a data frame interface that mimics data frame operations to access rows, columns, and subsets of rows and columns from the S4 objects of the enriched result. Users can use head and tail to print part of the result. The nrow, ncol, and dim methods are also supported to access basic information such as how many pathways are enriched.## head or tail to print first or last n rowshead(ego, 2)## ID Description GeneRatio BgRatio pvalue## GO:0140014 GO:0140014 mitotic nuclear division 34/194 286/18866 2.171838e-26## GO:0000280 GO:0000280 nuclear division 36/194 428/18866 1.099719e-22## p.adjust qvalue## GO:0140014 6.700119e-23 5.710790e-23## GO:0000280 1.696316e-19 1.445841e-19## geneID## GO:0140014 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/NCAPH/DLGAP5/UBE2C/NUSAP1/TPX2/TACC3/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1/BMP4## GO:0000280 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/NUSAP1/TPX2/TACC3/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1/BMP4## Count## GO:0140014 34## GO:0000280 36
