File:GseaTable.png
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Summary
data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000,
minSize=15, maxSize=100)
# I pick 5 pathways with + NES and 5 pathways with - NES.
fgseaRes[order(pval), ][62:71, c('pathway', 'NES')]
# pathway NES
# 1: 5992282_ECM_proteoglycans 1.984081
# 2: 5992219_Regulation_of_cholesterol_biosynthesis_by_SREBP_SREBF_ 1.955961
# 3: 5991505_Telomere_Maintenance 1.980520
# 4: 5991107_Pyrimidine_metabolism 1.935453
# 5: 5991359_Translesion_Synthesis_by_POLH 2.003523
# 6: 5991421_Effects_of_PIP2_hydrolysis -1.904118
# 7: 5992312_HDMs_demethylate_histones -1.909756
# 8: 5992327_HSF1-dependent_transactivation -1.927116
# 9: 5991838_Netrin-1_signaling -1.928526
#10: 5991547_RIG-I_MDA5_mediated_induction_of_IFN-alpha_beta_pathways -1.784904
topPathways <- fgseaRes[order(pval),][62:71, pathway]
plotGseaTable(examplePathways[topPathways], exampleRanks,
fgseaRes, gseaParam=0.5)
File history
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| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 11:01, 12 January 2023 | | 800 × 600 (81 KB) | Brb (talk | contribs) | <pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) # I pick 5 pathways with + NES and 5 pathways with - NES. fgseaRes[order(pval), ][62:71, c('pathway', 'NES')] # pathway NES # 1: 5992282_ECM_proteoglycans 1.984081 # 2: 5992219_Regulation_of_cholesterol_biosynthesis_by_SREBP_SREBF_ 1.95... |
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