Revert "Add tie handling"

.gitignore

@@ -5,7 +5,3 @@
 *.rds
 *.Rbin
 *.gz
-*.pdf
-*.csv
-*.csv
-*.pdf

DESCRIPTION

@@ -10,13 +10,25 @@ Authors@R: c(
 		 comment = c(ORCID = "0000-0001-8906-5270")))
 Description: Though there are many algorithms for enrichment analysis, most do not perform permutation statistics which do not rely on assumptions about the input distribution and do not allow for analysis of multiple omics data types. This tool enables users to input any omics data type as long as they provide corresponding set annotations or use the default gene set annotations. Users can also use this tool to prioritize drug mechanisms of action based on selective toxicity using drug mechanism enrichment analysis (https://belindabgarana.github.io/DMEA) as long as they provide expression data which corresponds to the input omics data type or use the default CCLE RNA-seq data (version 19Q4) and PRISM drug screen of 327 adherent cancer cell lines.
 License: MIT
-URL: https://github.com/PNNL-CompBio/panSEA
-BugReports: https://github.com/PNNL-CompBio/panSEA/issues
+URL: https://github.com/BelindaBGarana/panSEA
+BugReports: https://github.com/BelindaBGarana/panSEA/issues
 Encoding: UTF-8
-Depends: ggplot2 (>= 3.4.4)
 Imports:
 	ggplot2, DMEA, plyr, dplyr, Biobase, data.table, ggcorrplot, ggvenn, GSA, igraph, 
 	limma, metap, msigdbr, multtest, qvalue, reshape2, stats, stringr, viridis, visNetwork, utils
 VignetteBuilder: knitr
 Suggests: BiocStyle, knitr, rmarkdown
-RoxygenNote: 7.3.3
+Collate:
+	'mDEG.R'
+	'ssGSEA.R'
+	'DMEA_cell_corr.R'
+	'DMEA_gene_corr.R'
+	'compile_mDEG.R'
+	'compile_mGSEA.R'
+	'compile_mDMEA.R'
+	'mGSEA.R'
+	'mDMEA.R'
+	'mDMEA_cell_corr.R'
+	'mDMEA_gene_corr.R'
+	'netSEA.R'
+	'panSEA.R'

Examples/Coldren_metabolomics_DEGs.csv

@@ -0,0 +1,226 @@
+"Metabolite","Log2FC"
+"acetylcarnitine",-0.432566808333332
+"acetylcholine",0.0848597708333374
+"acetylglycine",0.157840045833336
+"aconitate",-0.127447645833334
+"adenine",0.0936795041666674
+"adenosine",0.0263129250000027
+"adipate",0.0499140708333332
+"alanine",0.058624316666668
+"allantoin",-0.147068362499999
+"alpha.glycerophosphate",-0.288459241666666
+"alpha.glycerophosphocholine",-0.380057358333332
+"alpha.hydroxybutyrate",0.0414708541666702
+"alpha.ketoglutarate",0.106047975000002
+"AMP",0.0345036250000037
+"anserine",0.00612032500000215
+"anthranilic.acid",-0.573772275
+"arachidonyl_carnitine",0.0517635541666701
+"arginine",-0.151282108333334
+"asparagine",-0.625436620833331
+"aspartate",-0.118030024999996
+"beta.alanine",-0.0878314624999978
+"betaine",-0.0747323833333304
+"butyrobetaine",-0.217442329166664
+"butyrylcarnitine.isobutyrylcarnitine",-0.185442416666666
+"C14.0.CE",-0.201016083333331
+"C14.0.LPC",0.193495700000001
+"C14.0.SM",0.0318908250000014
+"C16.0.CE",-0.0860768249999975
+"C16.0.LPC",-0.0582082916666637
+"C16.0.LPE",-0.106834108333332
+"C16.0.SM",0.0383061291666698
+"C16.1.CE",-0.213105058333332
+"C16.1.LPC",0.0121953375000006
+"C16.1.SM",-0.0237581416666659
+"C18.0.CE",-0.112483837499997
+"C18.0.LPC",-0.0505661749999966
+"C18.0.LPE",-0.0796807458333308
+"C18.0.SM",-0.138665979166664
+"C18.1.CE",-0.256277508333332
+"C18.1.LPC",-0.0934620666666648
+"C18.1.LPE",-0.0887394791666658
+"C18.1.SM",0.0525063541666686
+"C18.2.CE",-0.151707658333332
+"C18.2.LPC",0.0923146625000024
+"C18.2.SM",-0.0858089833333313
+"C18.3.CE",-0.149956962499997
+"C20.3.CE",-0.190236112499997
+"C20.3.LPC",-0.0293843999999979
+"C20.4.CE",-0.0871173249999986
+"C20.4.LPC",0.0415406208333344
+"C20.4.LPE",-0.00236039999999882
+"C20.5.CE",-0.166296941666665
+"C22.0.SM",0.0457310333333361
+"C22.1.SM",-0.0517156083333328
+"C22.6.CE",-0.226050570833332
+"C22.6.LPC",-0.0172023291666656
+"C22.6.LPE",0.136793895833336
+"C24.0.SM",-0.128569124999997
+"C24.1.SM",-0.0921815749999979
+"C32.0.PC",0.0554869708333348
+"C32.1.PC",0.0371743500000026
+"C32.2.PC",-0.071951416666665
+"C34.1.DAG",-0.0341589208333319
+"C34.1.PC",0.0376362250000026
+"C34.2.DAG",0.199680829166669
+"C34.2.PC",0.0245784041666663
+"C34.3.PC",-0.0580227166666658
+"C34.4.PC",0.0265971958333351
+"C36.1.DAG",0.0146541041666675
+"C36.1.PC",0.0190916333333373
+"C36.2.DAG",0.148854970833336
+"C36.2.PC",0.0188580125000026
+"C36.3.PC",-0.0718277958333315
+"C36.4.PC.A",-0.103299541666663
+"C36.4.PC.B",-0.0665448749999964
+"C38.2.PC",-0.012767795833331
+"C38.4.PC",0.0251847791666684
+"C38.5.PC",-0.0858348458333316
+"C38.6.PC",-0.115984387499998
+"C40.6.PC",0.0689353333333358
+"C46.0.TAG",0.0534822125000014
+"C46.1.TAG",0.120444508333335
+"C46.2.TAG",0.168058041666668
+"C48.0.TAG",-0.0120636916666639
+"C48.1.TAG",0.0866925250000019
+"C48.2.TAG",0.247110458333335
+"C48.3.TAG",0.121198904166668
+"C50.0.TAG",-0.090532370833329
+"C50.1.TAG",-0.0312308249999997
+"C50.2.TAG",0.14392116666667
+"C50.3.TAG",0.260920037500002
+"C52.1.TAG",0.0282836291666682
+"C52.2.TAG",0.0721745083333349
+"C52.3.TAG",0.211299400000001
+"C52.4.TAG",0.291782162500001
+"C52.5.TAG",0.186186879166669
+"C54.1.TAG",0.145608716666671
+"C54.2.TAG",0.113122495833332
+"C54.3.TAG",0.165381579166669
+"C54.4.TAG",0.318235354166669
+"C54.5.TAG",0.2507256625
+"C54.6.TAG",0.221204366666665
+"C54.7.TAG",0.143686108333338
+"C56.2.TAG",0.122194420833337
+"C56.3.TAG",0.190865941666667
+"C56.4.TAG",0.336044787500001
+"C56.5.TAG",0.326843391666668
+"C56.6.TAG",0.313725975000002
+"C56.7.TAG",0.131556641666669
+"C56.8.TAG",0.107675116666671
+"C58.6.TAG",0.282476175000001
+"C58.7.TAG",0.308793120833335
+"C58.8.TAG",0.137928808333336
+"cAMP",0.0830368166666684
+"carnitine",-0.177814479166663
+"carnosine",0.00257600000000036
+"choline",0.169593637500004
+"cis.trans.hydroxyproline",-0.545933629166664
+"citrate",-0.084288749999998
+"citrulline",-0.219306595833331
+"CMP",-0.0127537124999968
+"cotinine",0.00411665416666818
+"creatine",-0.00689356666666452
+"creatinine",-0.130710491666663
+"cystathionine",-0.11290623333333
+"cytidine",-0.216521862499998
+"dCMP",0.0360001041666687
+"DHAP.glyceraldehyde.3P",0.0356792791666685
+"dimethylglycine",-0.154732733333331
+"erythrose.4.phosphate",-0.0523152958333295
+"F1P.F6P.G1P.G6P",-0.0382475624999969
+"fumarate.maleate.alpha.ketoisovalerate",0.183663591666668
+"GABA",-0.106485483333331
+"glucuronate",0.101862387500004
+"glutamate",-0.00790752083333235
+"glutamine",0.477598212500003
+"glutathione.oxidized",-0.178272016666662
+"glutathione.reduced",-0.14519688333333
+"glycine",-0.0504685749999974
+"glycodeoxycholate.glycochenodeoxycholate",-0.0807517791666648
+"GMP",-0.10557725
+"guanosine",0.0197052583333344
+"heptanoylcarnitine",0.120376979166669
+"hexanoylcarnitine",-0.190520004166664
+"hexoses..HILIC.neg.",-0.139889699999999
+"hexoses..HILIC.pos.",0.0815303916666679
+"hippurate",-0.0880815583333288
+"histidine",0.0321703250000018
+"homocysteine",-0.456763658333331
+"hypoxanthine",-0.0190687291666647
+"inosine",0.0737183750000021
+"inositol",0.155007966666669
+"isocitrate",-0.0806645124999985
+"isoleucine",0.17260629166667
+"kynurenic.acid",-0.166509737499997
+"kynurenine",-0.0341685083333321
+"lactate",0.0522774875000032
+"lactose",-0.026702129166666
+"lauroylcarnitine",-0.101353045833335
+"leucine",0.0615382541666687
+"lysine",0.19088934166667
+"malate",0.186374954166667
+"malondialdehyde",0.0742086625000038
+"malonylcarnitine",-0.219188966666666
+"methionine",0.26556077916667
+"methionine.sulfoxide",-0.0882254041666641
+"myristoylcarnitine",-0.0374857749999951
+"N.carbamoyl.beta.alanine",0.00985656249999955
+"NAD",0.0373247958333351
+"NADP",-0.129011533333329
+"niacinamide",0.250893058333334
+"NMMA",-0.1059158875
+"oleylcarnitine",-0.0541690208333323
+"ornithine",-0.365185533333332
+"oxalate",0.12767516666667
+"palmitoylcarnitine",-0.063024412499999
+"pantothenate",-0.218344945833331
+"PEP",0.243672191666669
+"phenylalanine",0.161357450000002
+"phosphocreatine",-0.115935191666666
+"pipecolic.acid",-0.152780758333331
+"proline",-0.110353079166665
+"propionylcarnitine",-0.352922133333331
+"putrescine",-0.149027291666666
+"pyroglutamic.acid",0.0284851666666706
+"ribose.5.P.ribulose5.P",0.0654795958333345
+"sarcosine",-0.10880102083333
+"SDMA.ADMA",-0.190176537499998
+"serine",0.295831595833335
+"serotonin",0.0552602458333329
+"sorbitol",-0.0636386999999967
+"stearoylcarnitine",0.0951335583333348
+"succinate.methylmalonate",-0.103723762499999
+"sucrose",0.00522682500000116
+"taurine",-0.215636758333331
+"taurocholate",0.0419375750000004
+"taurodeoxycholate.taurochenodeoxycholate",-0.0820512999999989
+"thiamine",0.206043350000003
+"threonine",0.189575637500001
+"thymidine",-0.643547141666664
+"thymine",0.0567070458333356
+"thyroxine",-0.00779467083333074
+"trimethylamine.N.oxide",0.199691975000002
+"tryptophan",0.00439269166666723
+"tyrosine",0.121640591666667
+"UDP.galactose.UDP.glucose",-0.0511230458333332
+"UMP",0.0627405083333343
+"uracil",0.00209480833333853
+"urate",0.148778220833335
+"uridine",-0.00660626249999652
+"valerylcarnitine.isovalerylcarnitine.2.methylbutyroylcarnitine",0.094920475000003
+"valine",0.216623583333336
+"X1.methylnicotinamide",0.380228920833334
+"X2.aminoadipate",-0.148857954166664
+"X2.deoxyadenosine",-0.258411383333331
+"X2.deoxycytidine",-0.872290891666666
+"X2.hydroxyglutarate",0.113030700000001
+"X3.methyladipate.pimelate",0.0389818500000025
+"X3.phosphoglycerate",0.0838171791666689
+"X4.pyridoxate",0.132790212500002
+"X5.adenosylhomocysteine",0.151265704166669
+"X5.HIAA",-0.0473472458333308
+"X6.phosphogluconate",0.126974662500001
+"xanthine",-0.139633316666665
+"xanthosine",0.0225466583333356