File:GseaTable.png
Jump to navigation
Jump to search
GseaTable.png (800 × 600 pixels, file size: 81 KB, MIME type: image/png)
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
Click on a date/time to view the file as it appeared at that time.
Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 12:01, 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... |
You cannot overwrite this file.
File usage
The following page uses this file: