diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx index 7bd24a801baa7802164201f4c0d419330560a21d..c8c031be5b5b9ddb2c737a48ac204e11e67e00a4 100644 --- a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx +++ b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:418ee94bfb5c89f06b385367b042997416434a8b48b66d3adfa72aa100ea9af5 -size 27833 +oid sha256:cf318fbf37d75656e6e6405bf63a38948e519a50895975890edd21017315f01b +size 20715 diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/compound_rts_exclusion.csv b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/compound_rts_exclusion.csv new file mode 100644 index 0000000000000000000000000000000000000000..8dc7e72069458589a1e14fafa45f3d7e6800857e --- /dev/null +++ b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/compound_rts_exclusion.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a629afaad72b44d61f9baac755a6c9ed9eeb055766d9d291b673d21a4b1d1d7c +size 10996 diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/isa.dataset_temp.xlsx b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/isa.dataset_temp.xlsx index 270d5f18db8cc20042b209303be26c4e92266ecd..abee48902ff403853269a7ae728b660c8a12ff92 100644 --- a/assays/cmQTL_val1_GH_2020_GC_MS/dataset/isa.dataset_temp.xlsx +++ b/assays/cmQTL_val1_GH_2020_GC_MS/dataset/isa.dataset_temp.xlsx @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d63d90d0e4df45541ea52c0349c41dd82b4c320e98e4382d1728583401de1f5c -size 9962 +oid sha256:00ca802dab7c5daff8508945ada83b5bc938b2f8e46bd378267904aaf6ad7fe0 +size 10329 diff --git a/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx b/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx index 3939c75bfa417423559fd9330a1455b8b62364da..b8164b2d3765b2022354f54487473f2f9c124569 100644 Binary files a/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx and b/assays/cmQTL_val1_GH_2020_GC_MS/isa.assay.xlsx differ diff --git a/runs/GC-MS normalization/Image.RData b/runs/GC-MS normalization/Image.RData index 8be71b208442c3116797ce1ca7ca0cab18d3b75e..cf75ab8beb1894ff90766ec19ee500cb4e6bdaa4 100644 Binary files a/runs/GC-MS normalization/Image.RData and b/runs/GC-MS normalization/Image.RData differ diff --git a/runs/GC-MS normalization/_loess_fit.pdf b/runs/GC-MS normalization/_loess_fit.pdf index 7bfdd6326ceb485a60331fad6624b9d758d3557f..5f36959e27ac6385b5c58ef6b036cbb337f2692d 100644 Binary files a/runs/GC-MS normalization/_loess_fit.pdf and b/runs/GC-MS normalization/_loess_fit.pdf differ diff --git a/runs/GC-MS normalization/_loess_norm_fw_log.pdf b/runs/GC-MS normalization/_loess_norm_fw_log.pdf index 22ae1df4324951ec29e20aa70d41f420c9c7a5cc..cdd054fb9ee56c5f888fa68fb687c30f3cff8963 100644 Binary files a/runs/GC-MS normalization/_loess_norm_fw_log.pdf and b/runs/GC-MS normalization/_loess_norm_fw_log.pdf differ diff --git a/runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv index f35a5b82b5f8410b231c92e7de6629d94988db66..99cc505ff0c86eff466e617373f39a83061598d3 100644 --- a/runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv +++ b/runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv @@ -1,124 +1,124 @@ RT_mean,Compound_Name,component,met -10.96712788259958,Adenine,adenine_264_279_rt11.12,m_1 -17.09682105263158,Adenosine monophosphate,adenosine-5-monophosphate_169_315_rt17.,m_2 -8.951278825995807,L-2-Aminoadipic acid,adipic_acid_2-amino_260_217_9.05,m_3 -7.604067085953878,Adipic acid,adipic_acid_275_111_rt7.70,m_4 -3.277071129707113,Alanine,alanine_116_218_rt3.38,m_5 -5.679728033472804,Alanine_peak_2,alanine_188_262_rt5.78,m_6 -6.693018867924528,3-Cyano-L-alanine,alanine_3_cyano_141_100_rt6.78,m_7 -6.351236897274633,beta-Alanine,alanine_beta_248_290_rt6.44,m_8 -9.800459290187892,Arginine,arginine_157_256_rt9.92,m_9 -10.544372384937239,Ascorbic Acid,ascorbic_acid_332_449_rt10.66,m_10 -8.893842105263158,Asparagine_peak_2,asparagine_116_188_rt9.00,m_11 -7.7426778242677825,Asparagine,asparagine_188_216_rt7.84,m_12 -7.381691022964509,Aspartic acid,aspartic_acid_232_218_rt7.48,m_13 -8.639412997903564,4-Hydroxybenzoic acid,benzoic_acid-4-hydroxy_267_223_rt8.76,m_14 -5.5830125523012555,Benzoic Acid,benzoic_acid_179_105_rt5.69,m_15 -4.410817610062893,Benzyl Alcohol,benzyl_alcohol_165_135_rt4.53,m_16 -7.300876826722338,gamma-Aminobutyric acid,butyric_acid_4-amino_174_304_rt7.40,m_17 -8.93968487394958,Calystegin A3,calystegine_a3_167_216_rt9.05,m_18 -9.105491525423728,Calystegin B2,calystegine_b2_167_288_rt9.2,m_19 -11.071530398322851,4-Hydroxycinnamic acid,cinnamic_acid-4hyd-trans_249_293_rt11.20,m_20 -9.605574112734864,Citric Acid,citric_acid_273_375_rt9.72,m_21 -6.946247379454927,Decanoic acid,decanoic_acid_229_117_rt7.04,m_22 -10.120960334029228,Dehydroascorbic acid,dehydroascorbic_acid_316_173_rt10.24,m_23 -6.587272727272727,Erythritol,erythritol_217_293_rt6.68,m_24 -7.14,"(2R,3R)-2,3,4-trihydroxybutanoic acid",erythronic_acid_292_rt7.24,m_25 -4.531341719077568,Ethanolamine,ethanolamine_174_rt4.63,m_26 -12.42021052631579,Fructose-6-phosphate,fructose-6-phosphate_459_315_rt12.55,m_27 -12.44442105263158,Fructose-6-phosphate_peak_2,fructose-6-phosphate_459_315_rt12.57,m_28 -9.391169102296452,alpha-D-fructopyranose,fructose_307_217_rt9.48,m_29 -8.438305084745762,L-Fucose,fucose_117_160_rt8.54,m_30 -8.568482587064677,L-Fucose_peak_2,fucose_117_160_rt8.64,m_31 -5.9579035639413,Fumaric Acid,fumaric_acid_245_115_rt6.09,m_32 -15.250336134453782,Galactinol,galactinol_204_191_rt15.38,m_33 -15.362457983193277,Galactinol_peak_2,galactinol_204_191_rt15.50,m_34 -10.02077922077922,"L-Galactono-1,4-lactone",galactonic_acid_1-4-lacton_217_451_rt10.11,m_35 -10.111440501043841,NA,galactonic_o_gluconic_acid_333_157_10.24,m_36 -10.255135699373696,D-Galacturonic Acid,galacturonic_acid_333_160_rt10.41,m_37 -12.989031578947369,6-Phosphogluconic acid,gluconic_acid_6phosphate_299_387_rt13.13,m_38 -9.973242677824267,Methyl alpha-D-glucopyranoside,glucopyranoside_133_204_rt10.03,m_39 -9.0467,alpha-D-glucose-1-phosphate,glucose-1-phosphate_217_rt9.16,m_40 -12.52317894736842,Glucose 6-phosphate,glucose-6-phosphate_160_387_rt12.65,m_41 -12.631052631578948,Glucose 6-phosphate_peak_2,glucose-6-phosphate_160_387_rt12.76,m_42 -8.971058315334773,Levoglucosan,"glucose_1,6_ah_betaD_204_217_rt9.11",m_43 -9.557933194154488,D-Glucose,glucose_160_319_rt9.68,m_44 -9.68866388308977,D-Glucose_peak_2,glucose_160_rt9.81,m_45 -9.690730688935282,Glutamine_peak_2,glutamine_156_245_rt9.80,m_46 -7.9590794979079496,Glutamine,glutamine_227_203_rt8.06,m_47 -8.467190775681342,2-Oxoglutaric acid,glutaric_acid_2-oxo_198_288_rt8.57,m_48 -6.716771488469602,Glutaric acid,glutaric_acid_261_158_rt6.80,m_49 -5.532767295597484,"(2R)-2,3-Dihydroxypropanoic acid",glyceric_acid_292_189_rt5.63,m_50 -9.286813417190775,sn-Glycerol 3-phosphate,glycerol-3-phosphate_357_445_rt9.40,m_51 -4.660901467505241,Glycerol,glycerol_117_205_rt4.75,m_52 -3.592033542976939,Glycine,glycine_102_147_rt3.70,m_53 -5.205146443514645,Glycine_peak_2,glycine_174_248_rt.5.31,m_54 -3.2436058700209642,Glycolic acid,glycolic_acid_177_205_rt3.35,m_55 -4.242217573221757,Guanidine,guanidine_146_171_rt4.33,m_56 -10.381589958158996,L-Gulonolactone,gulonic_acid_1-4-lactone_333_466_rt10.49,m_57 -9.473131524008352,NA,hexose_307_217_rt9.58,m_58 -10.978577405857742,Histidine,histidine_154_254_rt11.10,m_59 +10.96712788259958,adenine,adenine_264_279_rt11.12,m_1 +17.09682105263158,adenosine-5-monophosphate,adenosine-5-monophosphate_169_315_rt17.,m_2 +8.951278825995807,2-aminoadipic_acid,adipic_acid_2-amino_260_217_9.05,m_3 +7.604067085953878,adipic_acid,adipic_acid_275_111_rt7.70,m_4 +3.277071129707113,L-alanine,alanine_116_218_rt3.38,m_5 +5.679728033472804,L-alanine_peak_2,alanine_188_262_rt5.78,m_6 +6.693018867924528,beta-cyano-L-alanine,alanine_3_cyano_141_100_rt6.78,m_7 +6.351236897274633,beta-alanine,alanine_beta_248_290_rt6.44,m_8 +9.800459290187892,L-arginine,arginine_157_256_rt9.92,m_9 +10.544372384937239,ascorbic_acid,ascorbic_acid_332_449_rt10.66,m_10 +8.893842105263158,L-asparagine_peak_2,asparagine_116_188_rt9.00,m_11 +7.7426778242677825,L-asparagine,asparagine_188_216_rt7.84,m_12 +7.381691022964509,L-aspartic_acid,aspartic_acid_232_218_rt7.48,m_13 +8.639412997903564,4-hydroxy-benzoic_acid,benzoic_acid-4-hydroxy_267_223_rt8.76,m_14 +5.5830125523012555,benzoic_acid,benzoic_acid_179_105_rt5.69,m_15 +4.410817610062893,benzyl_alchohol,benzyl_alcohol_165_135_rt4.53,m_16 +7.300876826722338,4-aminobutyric_acid,butyric_acid_4-amino_174_304_rt7.40,m_17 +8.93968487394958,calystegine_a_3,calystegine_a3_167_216_rt9.05,m_18 +9.105491525423728,calystegine_b_2,calystegine_b2_167_288_rt9.2,m_19 +11.071530398322851,4-hydroxy-cinnamic_acid,cinnamic_acid-4hyd-trans_249_293_rt11.20,m_20 +9.605574112734864,citric_acid,citric_acid_273_375_rt9.72,m_21 +6.946247379454927,decanoic_acid,decanoic_acid_229_117_rt7.04,m_22 +10.120960334029228,dehydroascorbic_acid,dehydroascorbic_acid_316_173_rt10.24,m_23 +6.587272727272727,erythritol,erythritol_217_293_rt6.68,m_24 +7.14,erythronic_acid,erythronic_acid_292_rt7.24,m_25 +4.531341719077568,ethanolamine,ethanolamine_174_rt4.63,m_26 +12.42021052631579,fructose-6-phosphate,fructose-6-phosphate_459_315_rt12.55,m_27 +12.44442105263158,fructose-6-phosphate_peak_2,fructose-6-phosphate_459_315_rt12.57,m_28 +9.391169102296452,fructose,fructose_307_217_rt9.48,m_29 +8.438305084745762,fucose,fucose_117_160_rt8.54,m_30 +8.568482587064677,fucose_peak_2,fucose_117_160_rt8.64,m_31 +5.9579035639413,fumaric_acid,fumaric_acid_245_115_rt6.09,m_32 +15.250336134453782,galactinol,galactinol_204_191_rt15.38,m_33 +15.362457983193277,galactinol_peak_2,galactinol_204_191_rt15.50,m_34 +10.02077922077922,galactonolactone,galactonic_acid_1-4-lacton_217_451_rt10.11,m_35 +10.111440501043841,galactonic_glucoronic_acid,galactonic_o_gluconic_acid_333_157_10.24,m_36 +10.255135699373696,galacturonic_acid,galacturonic_acid_333_160_rt10.41,m_37 +12.989031578947369,6-phosphogluconic_acid,gluconic_acid_6phosphate_299_387_rt13.13,m_38 +9.973242677824267,methyl_alpha-D-glucopyranoside,glucopyranoside_133_204_rt10.03,m_39 +9.0467,glucose 1-phosphate,glucose-1-phosphate_217_rt9.16,m_40 +12.52317894736842,glucose-6-phosphate,glucose-6-phosphate_160_387_rt12.65,m_41 +12.631052631578948,glucose-6-phosphate_peak_2,glucose-6-phosphate_160_387_rt12.76,m_42 +8.971058315334773,levoglucosan,"glucose_1,6_ah_betaD_204_217_rt9.11",m_43 +9.557933194154488,D-glucose,glucose_160_319_rt9.68,m_44 +9.68866388308977,D-glucose_peak_2,glucose_160_rt9.81,m_45 +9.690730688935282,L-glutamine_peak_2,glutamine_156_245_rt9.80,m_46 +7.9590794979079496,L-glutamine,glutamine_227_203_rt8.06,m_47 +8.467190775681342,oxoglutaric_acid,glutaric_acid_2-oxo_198_288_rt8.57,m_48 +6.716771488469602,glutaric_acid,glutaric_acid_261_158_rt6.80,m_49 +5.532767295597484,glyceric_acid,glyceric_acid_292_189_rt5.63,m_50 +9.286813417190775,glycerophosphoric_acid,glycerol-3-phosphate_357_445_rt9.40,m_51 +4.660901467505241,glycerol,glycerol_117_205_rt4.75,m_52 +3.592033542976939,L-glycine,glycine_102_147_rt3.70,m_53 +5.205146443514645,L-glycine_peak_2,glycine_174_248_rt.5.31,m_54 +3.2436058700209642,glycolic_acid,glycolic_acid_177_205_rt3.35,m_55 +4.242217573221757,guanidine,guanidine_146_171_rt4.33,m_56 +10.381589958158996,L-gulonolactone,gulonic_acid_1-4-lactone_333_466_rt10.49,m_57 +9.473131524008352,hexose,hexose_307_217_rt9.58,m_58 +10.978577405857742,L-histidine,histidine_154_254_rt11.10,m_59 6.554106382978723,L-homoserine,homoserine_218_128_rt6.64,m_60 -12.793263157894737,1D-myo-inositol 3-phosphate,inositol-1-phosphate-myo_299_318_rt12.92,m_61 -10.59623430962343,Inositol,inositol_myo_305_265_rt10.71,m_62 -9.687661795407099,Isocitric acid,isocitric_acid_245_rt9.80,m_63 -5.0997489539748955,l-Isoleucine,isoleucin_158_233_rt.5.21,m_64 -6.200649895178197,Itaconic Acid,itaconic_acid_147_259_rt6.32,m_65 -4.870774058577406,Leucine,leucine_158_232_rt4.97,m_66 -9.990897703549061,Lysine,lysine_156_174_rt10.07,m_67 -8.057372881355933,D-Lyxose,lyxose_xylose_307_217_rt8.16,m_68 -6.856885593220339,D-Citramalic acid,malic_acid_2-methyl_247_259_rt6.95,m_69 -7.1203549060542795,(2S)-2-Hydroxybutanedioic acid,malic_acid_233_245_rt7.22,m_70 -14.274117647058823,D-Cellobiose,malt_o_cellobiose_204_361_rt14.40,m_71 -14.114063157894737,D-(+)-Maltose,maltose_160_480_rt14.24,m_72 +12.793263157894737,myo-inositol_1-phosphate,inositol-1-phosphate-myo_299_318_rt12.92,m_61 +10.59623430962343,myo-inositol,inositol_myo_305_265_rt10.71,m_62 +9.687661795407099,isocitric_acid,isocitric_acid_245_rt9.80,m_63 +5.0997489539748955,L-isoleucine,isoleucin_158_233_rt.5.21,m_64 +6.200649895178197,itaconic_acid,itaconic_acid_147_259_rt6.32,m_65 +4.870774058577406,L-leucine,leucine_158_232_rt4.97,m_66 +9.990897703549061,L-lysine,lysine_156_174_rt10.07,m_67 +8.057372881355933,pectin,lyxose_xylose_307_217_rt8.16,m_68 +6.856885593220339,citramalic_acid,malic_acid_2-methyl_247_259_rt6.95,m_69 +7.1203549060542795,malic_acid,malic_acid_233_245_rt7.22,m_70 +14.274117647058823,cellobiose,malt_o_cellobiose_204_361_rt14.40,m_71 +14.114063157894737,D-maltose,maltose_160_480_rt14.24,m_72 9.017880952380953,Methyl alpha-D-mannopyranoside,mannopyr-1-o-m_133_204_rt9.14,m_73 -7.659707112970711,Methionine,methionine_176_128_rt7.76,m_74 -6.215723270440251,Nicotinic Acid,nicotinic_acid_180_136_rt6.32,m_75 -8.119329140461216,6-Hydroxynicotinic acid,nicotinic_acid_6-hydroxy_268_282_rt8.22,m_76 -6.113661087866109,Nonanoic Acid,nonanoic_acid_117_215_rt6.19,m_77 -9.227014613778707,L-ornithine_peak_2,ornithine_142_174_rt9.34,m_78 -7.922327044025157,L-ornithine,ornithine_142_348_rt8.03,m_79 -14.817079831932773,Palatinose,palatinose_204_361_rt14.95,m_80 -8.581820083682008,Phenylalanine,phenylalanine_192_266_rt8.69,m_81 -5.346075156576201,Phosphoric Acid,phosphoric_acid_314_299_rt.5.43,m_82 -6.014372384937238,l-Pipecolic acid,pipecolic_acid_156_230_rt6.11,m_83 -5.428870292887029,Proline,proline_142_130_rt.5.53,m_84 -7.25062893081761,Hydroxyproline,proline_4-hydroxy_230_140_rt7.34,m_85 -8.362887029288702,"1,4-Diaminobutane",putrescine_174_361_rt8.47,m_86 -3.206548117154812,2-Hydroxypyridine,pyridine-2-hydroxy_152_167_rt3.31,m_87 -4.69475890985325,4-Hydroxypyridine,pyridine_4-hydroxy_152_167_rt4.79,m_88 -8.187933194154489,L-Pyroglutamic acid,pyroglutamic_acid_156_258_rt8.30,m_89 -3.501194968553459,Pyruvic acid,pyruvic_acid_174_189_rt3.61,m_90 -9.370855949895615,Quinic acid,quinic_acid_255_345_rt9.45,m_91 -16.659684210526315,Chlorogenic Acid,quinic_acid_3-caffeoyl-trans_345_255_rt16.8,m_92 -16.904147368421054,Raffinose,raffinose_437_451_rt16.91,m_93 -8.304651162790698,L-Rhamnose,rhamnose_117_160_rt8.43,m_94 -8.100168421052631,NA,ribitol_217_rt8.20,m_95 -8.101863207547169,NA,ribitol_319_rt8.20,m_96 -6.595094339622642,O-acetyl-L-serine,serine-o-acetyl_174_132_rt6.69,m_97 -5.737071129707113,Serine,serine_204_218_rt5.84,m_98 -9.461022964509395,Shikimic acid,shikimic_acid_204_462_rt9.57,m_99 -11.712526315789473,Spermidine,spermidine_174_144_11.85,m_100 -11.787578947368422,Spermidine_peak_2,spermidine_174_200_rt11.94,m_101 -5.866289308176101,Succinic Acid,succinic_acid_247_172_5.97,m_102 -13.638846960167715,Sucrose_peak_2,sucrose2_204_361_rt13.79,m_103 -13.638385744234801,Sucrose,sucrose_437_361_rt13.77,m_104 -10.002578616352201,Myristic acid,tetradecanoic_acid_285_300_rt10.09,m_105 -7.392852852852853,L-threonic acid,threonic_acid_292_220_rt7.49,m_106 +7.659707112970711,L-methionine,methionine_176_128_rt7.76,m_74 +6.215723270440251,nicotinic_acid,nicotinic_acid_180_136_rt6.32,m_75 +8.119329140461216,6-hydroxy-nicotinic_acid,nicotinic_acid_6-hydroxy_268_282_rt8.22,m_76 +6.113661087866109,nonanoic_acid,nonanoic_acid_117_215_rt6.19,m_77 +9.227014613778707,ornithine_peak_2,ornithine_142_174_rt9.34,m_78 +7.922327044025157,ornithine,ornithine_142_348_rt8.03,m_79 +14.817079831932773,palatinose,palatinose_204_361_rt14.95,m_80 +8.581820083682008,L-phenylalanine,phenylalanine_192_266_rt8.69,m_81 +5.346075156576201,phosphate,phosphoric_acid_314_299_rt.5.43,m_82 +6.014372384937238,L-pipecolic acid,pipecolic_acid_156_230_rt6.11,m_83 +5.428870292887029,L-proline,proline_142_130_rt.5.53,m_84 +7.25062893081761,4-hydroxyproline,proline_4-hydroxy_230_140_rt7.34,m_85 +8.362887029288702,1_4-diaminobutane,putrescine_174_361_rt8.47,m_86 +3.206548117154812,2-hydroxypyridine,pyridine-2-hydroxy_152_167_rt3.31,m_87 +4.69475890985325,4-hydroxypyridine,pyridine_4-hydroxy_152_167_rt4.79,m_88 +8.187933194154489,pyroglutamic_acid,pyroglutamic_acid_156_258_rt8.30,m_89 +3.501194968553459,pyruvic_acid,pyruvic_acid_174_189_rt3.61,m_90 +9.370855949895615,quinic_acid,quinic_acid_255_345_rt9.45,m_91 +16.659684210526315,chlorogenic_acid,quinic_acid_3-caffeoyl-trans_345_255_rt16.8,m_92 +16.904147368421054,raffinose,raffinose_437_451_rt16.91,m_93 +8.304651162790698,rhamnose,rhamnose_117_160_rt8.43,m_94 +8.100168421052631,ribitol,ribitol_217_rt8.20,m_95 +8.101863207547169,ribitol_peak_2,ribitol_319_rt8.20,m_96 +6.595094339622642,O-acetylserine,serine-o-acetyl_174_132_rt6.69,m_97 +5.737071129707113,L-serine,serine_204_218_rt5.84,m_98 +9.461022964509395,shikimic_acid,shikimic_acid_204_462_rt9.57,m_99 +11.712526315789473,spermidine,spermidine_174_144_11.85,m_100 +11.787578947368422,spermidine_peak_2,spermidine_174_200_rt11.94,m_101 +5.866289308176101,succinic_acid,succinic_acid_247_172_5.97,m_102 +13.638846960167715,sucrose_peak_2,sucrose2_204_361_rt13.79,m_103 +13.638385744234801,sucrose,sucrose_437_361_rt13.77,m_104 +10.002578616352201,myristic_acid,tetradecanoic_acid_285_300_rt10.09,m_105 +7.392852852852853,threonic_acid,threonic_acid_292_220_rt7.49,m_106 5.902238493723849,L-threonine,threonine_219_291_rt6.01,m_107 -14.213707865168539,Trehalose,trehalose_alpha_alpha_191_169_rt14.33,m_108 -13.209157894736842,Tryptophan_peak_2,tryptophan_130_218_rt13.35,m_109 -12.811029411764705,Tryptophan,tryptophan_202_291_rt12.94,m_110 -10.336673640167364,Tyramine,tyramine_174_338_rt10.45,m_111 -10.65112970711297,Tyrosine,tyrosine_218_280_rt10.78,m_112 -15.950926315789474,NA,unknown(sugar)_361_217_rt16.08,m_113 -6.513102725366876,NA,unknown_102_306_rt6.60,m_114 -4.057092050209205,NA,unknown_103_89_rt4.17,m_115 -7.567719665271967,NA,unknown_155_217_rt7.68,m_116 -8.404020887728459,NA,unknown_217_117_rt8.49,m_117 -10.292150313152401,Dehydroascorbic acid_peak_2,unknown_dhascorbicacid_173_316_rt.10.41,m_118 -12.21663157894737,Sinapic acid,unknown_sinap_acid_trans_338_368_rt12.32,m_119 -6.316205450733753,Uracil,uracil_241_255_rt6.41,m_120 -5.4569874476987446,Urea,urea_189_204_rt5.56,m_121 -4.326589958158996,Valine,valine_144_218_rt4.42,m_122 -7.97891592920354,D-xylopyranose,xylose_307_217_rt8.06,m_123 +14.213707865168539,trehalose,trehalose_alpha_alpha_191_169_rt14.33,m_108 +13.209157894736842,L-tryptophan_peak_2,tryptophan_130_218_rt13.35,m_109 +12.811029411764705,L-tryptophan,tryptophan_202_291_rt12.94,m_110 +10.336673640167364,tyramine,tyramine_174_338_rt10.45,m_111 +10.65112970711297,L-tyrosine,tyrosine_218_280_rt10.78,m_112 +15.950926315789474,unannotated_peak_5,unknown(sugar)_361_217_rt16.08,m_113 +6.513102725366876,unannotated_peak_2,unknown_102_306_rt6.60,m_114 +4.057092050209205,unannotated,unknown_103_89_rt4.17,m_115 +7.567719665271967,unannotated_peak_3,unknown_155_217_rt7.68,m_116 +8.404020887728459,unannotated_peak_4,unknown_217_117_rt8.49,m_117 +10.292150313152401,dehydroascorbic_acid_peak_2,unknown_dhascorbicacid_173_316_rt.10.41,m_118 +12.21663157894737,sinapic_acid,unknown_sinap_acid_trans_338_368_rt12.32,m_119 +6.316205450733753,uracil,uracil_241_255_rt6.41,m_120 +5.4569874476987446,urea,urea_189_204_rt5.56,m_121 +4.326589958158996,L-valine,valine_144_218_rt4.42,m_122 +7.97891592920354,D-Xylose,xylose_307_217_rt8.06,m_123 diff --git a/runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv index 553f0861cc67b0b8b490dd21fde99b537bf301c3..2b2523c272566afd6efc523a7e0786a550660bf3 100644 --- a/runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv +++ b/runs/GC-MS normalization/cmQTL_val_1_2_miss_GC.csv @@ -1229,495 +1229,249 @@ exp,met,tissue,treatment,na,n,percent_na 1,m_99,leaf,0.8,0,24,0 1,m_99,leaf,1,0,24,0 1,m_99,leaf,NA,0,21,0 -2,m_1,fruit,1,0,58,0 -2,m_1,fruit,NA,0,25,0 -2,m_1,leaf,1,0,30,0 -2,m_1,leaf,NA,0,7,0 -2,m_10,fruit,1,0,58,0 -2,m_10,fruit,NA,0,25,0 -2,m_10,leaf,1,0,30,0 -2,m_10,leaf,NA,0,7,0 -2,m_100,fruit,1,0,58,0 -2,m_100,fruit,NA,0,25,0 -2,m_100,leaf,1,0,30,0 -2,m_100,leaf,NA,0,7,0 -2,m_101,fruit,1,0,58,0 -2,m_101,fruit,NA,0,25,0 -2,m_101,leaf,1,0,30,0 -2,m_101,leaf,NA,0,7,0 -2,m_102,fruit,1,0,58,0 -2,m_102,fruit,NA,0,25,0 -2,m_102,leaf,1,0,30,0 -2,m_102,leaf,NA,0,7,0 -2,m_103,fruit,1,0,58,0 -2,m_103,fruit,NA,0,25,0 -2,m_103,leaf,1,0,30,0 -2,m_103,leaf,NA,0,7,0 -2,m_104,fruit,1,0,58,0 -2,m_104,fruit,NA,0,25,0 -2,m_104,leaf,1,0,30,0 -2,m_104,leaf,NA,0,7,0 -2,m_105,fruit,1,0,58,0 -2,m_105,fruit,NA,0,25,0 -2,m_105,leaf,1,0,30,0 -2,m_105,leaf,NA,0,7,0 -2,m_106,fruit,1,24,58,41.37931034482759 -2,m_106,fruit,NA,6,25,24 -2,m_106,leaf,1,0,30,0 -2,m_106,leaf,NA,1,7,14.285714285714285 -2,m_107,fruit,1,0,58,0 -2,m_107,fruit,NA,0,25,0 -2,m_107,leaf,1,0,30,0 -2,m_107,leaf,NA,0,7,0 -2,m_108,fruit,1,5,58,8.620689655172415 -2,m_108,fruit,NA,2,25,8 -2,m_108,leaf,1,0,30,0 -2,m_108,leaf,NA,0,7,0 -2,m_109,fruit,1,0,58,0 -2,m_109,fruit,NA,0,25,0 -2,m_109,leaf,1,0,30,0 -2,m_109,leaf,NA,0,7,0 -2,m_11,fruit,1,20,58,34.48275862068966 -2,m_11,fruit,NA,5,25,20 -2,m_11,leaf,1,2,30,6.666666666666667 -2,m_11,leaf,NA,2,7,28.57142857142857 -2,m_110,fruit,1,0,58,0 -2,m_110,fruit,NA,0,25,0 -2,m_110,leaf,1,0,30,0 -2,m_110,leaf,NA,0,7,0 -2,m_111,fruit,1,0,58,0 -2,m_111,fruit,NA,0,25,0 -2,m_111,leaf,1,0,30,0 -2,m_111,leaf,NA,0,7,0 -2,m_112,fruit,1,0,58,0 -2,m_112,fruit,NA,0,25,0 -2,m_112,leaf,1,0,30,0 -2,m_112,leaf,NA,0,7,0 -2,m_113,fruit,1,0,58,0 -2,m_113,fruit,NA,0,25,0 -2,m_113,leaf,1,0,30,0 -2,m_113,leaf,NA,0,7,0 -2,m_114,fruit,1,0,58,0 -2,m_114,fruit,NA,0,25,0 -2,m_114,leaf,1,0,30,0 -2,m_114,leaf,NA,0,7,0 -2,m_115,fruit,1,0,58,0 -2,m_115,fruit,NA,0,25,0 -2,m_115,leaf,1,0,30,0 -2,m_115,leaf,NA,0,7,0 -2,m_116,fruit,1,0,58,0 -2,m_116,fruit,NA,0,25,0 -2,m_116,leaf,1,0,30,0 -2,m_116,leaf,NA,0,7,0 -2,m_117,fruit,1,19,58,32.758620689655174 -2,m_117,fruit,NA,10,25,40 -2,m_117,leaf,1,0,30,0 -2,m_117,leaf,NA,0,7,0 -2,m_118,fruit,1,0,58,0 -2,m_118,fruit,NA,0,25,0 -2,m_118,leaf,1,0,30,0 -2,m_118,leaf,NA,0,7,0 -2,m_119,fruit,1,0,58,0 -2,m_119,fruit,NA,0,25,0 -2,m_119,leaf,1,0,30,0 -2,m_119,leaf,NA,0,7,0 -2,m_12,fruit,1,0,58,0 -2,m_12,fruit,NA,0,25,0 -2,m_12,leaf,1,0,30,0 -2,m_12,leaf,NA,0,7,0 -2,m_120,fruit,1,0,58,0 -2,m_120,fruit,NA,0,25,0 -2,m_120,leaf,1,0,30,0 -2,m_120,leaf,NA,0,7,0 -2,m_121,fruit,1,0,58,0 -2,m_121,fruit,NA,0,25,0 -2,m_121,leaf,1,0,30,0 -2,m_121,leaf,NA,0,7,0 -2,m_122,fruit,1,0,58,0 -2,m_122,fruit,NA,0,25,0 -2,m_122,leaf,1,0,30,0 -2,m_122,leaf,NA,0,7,0 -2,m_123,fruit,1,8,58,13.793103448275861 -2,m_123,fruit,NA,2,25,8 -2,m_123,leaf,1,0,30,0 -2,m_123,leaf,NA,0,7,0 -2,m_13,fruit,1,0,58,0 -2,m_13,fruit,NA,0,25,0 -2,m_13,leaf,1,0,30,0 -2,m_13,leaf,NA,0,7,0 -2,m_14,fruit,1,0,58,0 -2,m_14,fruit,NA,0,25,0 -2,m_14,leaf,1,0,30,0 -2,m_14,leaf,NA,0,7,0 -2,m_15,fruit,1,0,58,0 -2,m_15,fruit,NA,0,25,0 -2,m_15,leaf,1,0,30,0 -2,m_15,leaf,NA,0,7,0 -2,m_16,fruit,1,0,58,0 -2,m_16,fruit,NA,0,25,0 -2,m_16,leaf,1,0,30,0 -2,m_16,leaf,NA,0,7,0 -2,m_17,fruit,1,0,58,0 -2,m_17,fruit,NA,0,25,0 -2,m_17,leaf,1,0,30,0 -2,m_17,leaf,NA,0,7,0 -2,m_18,fruit,1,0,58,0 -2,m_18,fruit,NA,0,25,0 -2,m_18,leaf,1,0,30,0 -2,m_18,leaf,NA,0,7,0 -2,m_19,fruit,1,33,58,56.896551724137936 -2,m_19,fruit,NA,18,25,72 -2,m_19,leaf,1,0,30,0 -2,m_19,leaf,NA,1,7,14.285714285714285 -2,m_2,fruit,1,0,58,0 -2,m_2,fruit,NA,0,25,0 -2,m_2,leaf,1,0,30,0 -2,m_2,leaf,NA,0,7,0 -2,m_20,fruit,1,0,58,0 -2,m_20,fruit,NA,0,25,0 -2,m_20,leaf,1,0,30,0 -2,m_20,leaf,NA,0,7,0 -2,m_21,fruit,1,0,58,0 -2,m_21,fruit,NA,0,25,0 -2,m_21,leaf,1,0,30,0 -2,m_21,leaf,NA,0,7,0 -2,m_22,fruit,1,0,58,0 -2,m_22,fruit,NA,0,25,0 -2,m_22,leaf,1,0,30,0 -2,m_22,leaf,NA,0,7,0 -2,m_23,fruit,1,0,58,0 -2,m_23,fruit,NA,0,25,0 -2,m_23,leaf,1,0,30,0 -2,m_23,leaf,NA,0,7,0 -2,m_24,fruit,1,0,58,0 -2,m_24,fruit,NA,0,25,0 -2,m_24,leaf,1,2,30,6.666666666666667 -2,m_24,leaf,NA,0,7,0 -2,m_25,fruit,1,0,58,0 -2,m_25,fruit,NA,0,25,0 -2,m_25,leaf,1,0,30,0 -2,m_25,leaf,NA,0,7,0 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+2,m_67,fruit,NA,0,32,0 +2,m_68,fruit,1,1,88,1.1363636363636365 +2,m_68,fruit,NA,0,32,0 +2,m_69,fruit,1,0,88,0 +2,m_69,fruit,NA,0,32,0 +2,m_7,fruit,1,0,88,0 +2,m_7,fruit,NA,0,32,0 +2,m_70,fruit,1,0,88,0 +2,m_70,fruit,NA,0,32,0 +2,m_71,fruit,1,0,88,0 +2,m_71,fruit,NA,0,32,0 +2,m_72,fruit,1,0,88,0 +2,m_72,fruit,NA,0,32,0 +2,m_73,fruit,1,16,88,18.181818181818183 +2,m_73,fruit,NA,4,32,12.5 +2,m_74,fruit,1,0,88,0 +2,m_74,fruit,NA,0,32,0 +2,m_75,fruit,1,0,88,0 +2,m_75,fruit,NA,0,32,0 +2,m_76,fruit,1,0,88,0 +2,m_76,fruit,NA,0,32,0 +2,m_77,fruit,1,0,88,0 +2,m_77,fruit,NA,0,32,0 +2,m_78,fruit,1,0,88,0 +2,m_78,fruit,NA,0,32,0 +2,m_79,fruit,1,0,88,0 +2,m_79,fruit,NA,0,32,0 +2,m_8,fruit,1,0,88,0 +2,m_8,fruit,NA,0,32,0 +2,m_80,fruit,1,0,88,0 +2,m_80,fruit,NA,0,32,0 +2,m_81,fruit,1,0,88,0 +2,m_81,fruit,NA,0,32,0 +2,m_82,fruit,1,0,88,0 +2,m_82,fruit,NA,0,32,0 +2,m_83,fruit,1,0,88,0 +2,m_83,fruit,NA,0,32,0 +2,m_84,fruit,1,0,88,0 +2,m_84,fruit,NA,0,32,0 +2,m_85,fruit,1,0,88,0 +2,m_85,fruit,NA,0,32,0 +2,m_86,fruit,1,0,88,0 +2,m_86,fruit,NA,0,32,0 +2,m_87,fruit,1,0,88,0 +2,m_87,fruit,NA,0,32,0 +2,m_88,fruit,1,0,88,0 +2,m_88,fruit,NA,0,32,0 +2,m_89,fruit,1,0,88,0 +2,m_89,fruit,NA,0,32,0 +2,m_9,fruit,1,0,88,0 +2,m_9,fruit,NA,0,32,0 +2,m_90,fruit,1,0,88,0 +2,m_90,fruit,NA,0,32,0 +2,m_91,fruit,1,0,88,0 +2,m_91,fruit,NA,0,32,0 +2,m_92,fruit,1,0,88,0 +2,m_92,fruit,NA,0,32,0 +2,m_93,fruit,1,0,88,0 +2,m_93,fruit,NA,0,32,0 +2,m_94,fruit,1,5,88,5.681818181818182 +2,m_94,fruit,NA,0,32,0 +2,m_95,fruit,1,0,88,0 +2,m_95,fruit,NA,0,32,0 +2,m_96,fruit,1,19,88,21.59090909090909 +2,m_96,fruit,NA,5,32,15.625 +2,m_97,fruit,1,0,88,0 +2,m_97,fruit,NA,0,32,0 +2,m_98,fruit,1,0,88,0 +2,m_98,fruit,NA,0,32,0 +2,m_99,fruit,1,0,88,0 +2,m_99,fruit,NA,0,32,0 diff --git a/runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv b/runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv index 90b43942f8e4f6e9a25e85b83f5c2e1ee41b5e1b..84807401b7ff038d78da9cc441bf444dd27f1654 100644 --- a/runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv +++ b/runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv @@ -436,43 +436,43 @@ NA,NA,NA,NA,leaf,NA,NA,NA,NA,1,e_0_1,5,NA,Pooled Sample,423,21111rA_44,21111rA_4 2441803_l,967514 MM WT,2441803,0.4,leaf,52,MoneyMaker,s_19,s_19,1,e_96_1,5,NA,Sample,435,21111rA_56,21111rA_56,56 NA,NA,NA,NA,leaf,NA,NA,NA,NA,1,e_0_1,5,NA,Pooled Sample,436,21111rA_57,21111rA_57,57 NA,NA,NA,NA,leaf,NA,NA,NA,NA,1,e_0_1,5,NA,Pooled Sample,437,21111rA_58,21111rA_58,58 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,438,21111rA_59,21111rA_59,1 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,439,21111rA_60,21111rA_60,2 -2493689_l,1016561 Sl10g086190 #21,2493689,1,leaf,50,adk1-1,s_221,s_221,2,e_1_2,6,NA,Sample,440,21111rA_61,21111rA_61,3 -2493690_l,1016561 Sl10g086190 #21,2493690,1,leaf,51.6,adk1-1,s_222,s_222,2,e_2_2,6,NA,Sample,441,21111rA_62,21111rA_62,4 -2493689_l,1016561 Sl10g086190 #21,2493689,1,leaf,54.5,adk1-1,s_219,s_219,2,e_3_2,6,NA,Sample,442,21111rA_63,21111rA_63,5 -2493597_l,1018727 Sl10g074630 #38,2493597,1,leaf,47.3,arlb1-1,s_208,s_208,2,e_4_2,6,NA,Sample,443,21111rA_64,21111rA_64,6 -2493596_l,1018727 Sl10g074630 #38,2493596,1,leaf,48.5,arlb1-1,s_207,s_207,2,e_5_2,6,NA,Sample,444,21111rA_65,21111rA_65,7 -2493615_l,1018728 74630#38.2,2493615,1,leaf,46.3,arlb1-2,s_210,s_210,2,e_6_2,6,NA,Sample,445,21111rA_66,21111rA_66,8 -2493632_l,1018728 74630#38.2,2493632,1,leaf,45.8,arlb1-2,s_212,s_212,2,e_7_2,6,NA,Sample,446,21111rA_67,21111rA_67,9 -2493542_l,1018733 MM WT,2493542,1,leaf,49.4,MoneyMaker,s_197,s_197,2,e_8_2,6,NA,Sample,447,21111rA_68,21111rA_68,10 -2493638_l,1018728 74630#38.2,2493638,1,leaf,51.5,arlb1-2,s_215,s_215,2,e_9_2,6,NA,Sample,448,21111rA_69,21111rA_69,11 -2493540_l,1018733 MM WT,2493540,1,leaf,52.8,MoneyMaker,s_195,s_195,2,e_10_2,6,NA,Sample,449,21111rA_70,21111rA_70,12 -2493595_l,1018727 Sl10g074630 #38,2493595,1,leaf,48.7,arlb1-1,s_206,s_206,2,e_11_2,6,NA,Sample,450,21111rA_71,21111rA_71,13 -2493629_l,1018728 74630#38.2,2493629,1,leaf,48.2,arlb1-2,s_211,s_211,2,e_12_2,6,NA,Sample,451,21111rA_72,21111rA_72,14 -2493541_l,1018733 MM WT,2493541,1,leaf,48.8,MoneyMaker,s_196,s_196,2,e_13_2,6,NA,Sample,452,21111rA_73,21111rA_73,15 -2493633_l,1018728 74630#38.2,2493633,1,leaf,47.2,arlb1-2,s_213,s_213,2,e_14_2,6,NA,Sample,453,21111rA_74,21111rA_74,16 -2493690_l,1016561 Sl10g086190 #21,2493690,1,leaf,51.1,adk1-1,s_220,s_220,2,e_15_2,6,NA,Sample,454,21111rA_75,21111rA_75,17 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,455,21111rA_76,21111rA_76,18 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,456,21111rA_77,21111rA_77,19 -2493591_l,1018727 Sl10g074630 #38,2493591,1,leaf,53,arlb1-1,s_202,s_202,2,e_16_2,6,NA,Sample,457,21111rA_78,21111rA_78,20 -2493593_l,1018727 Sl10g074630 #38,2493593,1,leaf,51.8,arlb1-1,s_204,s_204,2,e_17_2,6,NA,Sample,458,21111rA_79,21111rA_79,21 -2493634_l,1018728 74630#38.2,2493634,1,leaf,53.6,arlb1-2,s_214,s_214,2,e_18_2,6,NA,Sample,459,21111rA_80,21111rA_80,22 -2493592_l,1018727 Sl10g074630 #38,2493592,1,leaf,50.6,arlb1-1,s_203,s_203,2,e_19_2,6,NA,Sample,460,21111rA_81,21111rA_81,23 -2493538_l,1018733 MM WT,2493538,1,leaf,38.1,MoneyMaker,s_193,s_193,2,e_20_2,6,NA,Sample,461,21111rA_82,21111rA_82,24 -2493544_l,1018733 MM WT,2493544,1,leaf,48.9,MoneyMaker,s_199,s_199,2,e_21_2,6,NA,Sample,462,21111rA_83,21111rA_83,25 -2493641_l,1018728 74630#38.2,2493641,1,leaf,50.6,arlb1-2,s_217,s_217,2,e_22_2,6,NA,Sample,463,21111rA_84,21111rA_84,26 -2493564_l,1018732 Sl10g007340#10,2493564,1,leaf,50.8,up1-1,s_201,s_201,2,e_23_2,6,NA,Sample,464,21111rA_85,21111rA_85,27 -2493539_l,1018733 MM WT,2493539,1,leaf,47.1,MoneyMaker,s_194,s_194,2,e_24_2,6,NA,Sample,465,21111rA_86,21111rA_86,28 -2493545_l,1018733 MM WT,2493545,1,leaf,46.8,MoneyMaker,s_200,s_200,2,e_25_2,6,NA,Sample,466,21111rA_87,21111rA_87,29 -2493643_l,1018728 74630#38.2,2493643,1,leaf,53.3,arlb1-2,s_218,s_218,2,e_26_2,6,NA,Sample,467,21111rA_88,21111rA_88,30 -2493543_l,1018733 MM WT,2493543,1,leaf,53.7,MoneyMaker,s_198,s_198,2,e_27_2,6,NA,Sample,468,21111rA_89,21111rA_89,31 -2493640_l,1018728 74630#38.2,2493640,1,leaf,52.1,arlb1-2,s_216,s_216,2,e_28_2,6,NA,Sample,469,21111rA_90,21111rA_90,32 -2493598_l,1018727 Sl10g074630 #38,2493598,1,leaf,46.1,arlb1-1,s_209,s_209,2,e_29_2,6,NA,Sample,470,21111rA_91,21111rA_91,33 -2493594_l,1018727 Sl10g074630 #38,2493594,1,leaf,47.7,arlb1-1,s_205,s_205,2,e_30_2,6,NA,Sample,471,21111rA_92,21111rA_92,34 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,472,21111rA_93,21111rA_93,35 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,473,21111rA_94,21111rA_94,36 -NA,NA,NA,NA,leaf,NA,NA,NA,NA,2,e_-1_2,6,NA,blank sample,474,21111rA_95,21111rA_95,37 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,438,21111rA_59,21111rA_59,1 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,439,21111rA_60,21111rA_60,2 +2493689_l,1016561 Sl10g086190 #21,2493689,1,fruit,50,adk1-1,s_221,s_221,2,e_1_2,6,NA,Sample,440,21111rA_61,21111rA_61,3 +2493690_l,1016561 Sl10g086190 #21,2493690,1,fruit,51.6,adk1-1,s_222,s_222,2,e_2_2,6,NA,Sample,441,21111rA_62,21111rA_62,4 +2493689_l,1016561 Sl10g086190 #21,2493689,1,fruit,54.5,adk1-1,s_219,s_219,2,e_3_2,6,NA,Sample,442,21111rA_63,21111rA_63,5 +2493597_l,1018727 Sl10g074630 #38,2493597,1,fruit,47.3,arlb1-1,s_208,s_208,2,e_4_2,6,NA,Sample,443,21111rA_64,21111rA_64,6 +2493596_l,1018727 Sl10g074630 #38,2493596,1,fruit,48.5,arlb1-1,s_207,s_207,2,e_5_2,6,NA,Sample,444,21111rA_65,21111rA_65,7 +2493615_l,1018728 74630#38.2,2493615,1,fruit,46.3,arlb1-2,s_210,s_210,2,e_6_2,6,NA,Sample,445,21111rA_66,21111rA_66,8 +2493632_l,1018728 74630#38.2,2493632,1,fruit,45.8,arlb1-2,s_212,s_212,2,e_7_2,6,NA,Sample,446,21111rA_67,21111rA_67,9 +2493542_l,1018733 MM WT,2493542,1,fruit,49.4,MoneyMaker,s_197,s_197,2,e_8_2,6,NA,Sample,447,21111rA_68,21111rA_68,10 +2493638_l,1018728 74630#38.2,2493638,1,fruit,51.5,arlb1-2,s_215,s_215,2,e_9_2,6,NA,Sample,448,21111rA_69,21111rA_69,11 +2493540_l,1018733 MM WT,2493540,1,fruit,52.8,MoneyMaker,s_195,s_195,2,e_10_2,6,NA,Sample,449,21111rA_70,21111rA_70,12 +2493595_l,1018727 Sl10g074630 #38,2493595,1,fruit,48.7,arlb1-1,s_206,s_206,2,e_11_2,6,NA,Sample,450,21111rA_71,21111rA_71,13 +2493629_l,1018728 74630#38.2,2493629,1,fruit,48.2,arlb1-2,s_211,s_211,2,e_12_2,6,NA,Sample,451,21111rA_72,21111rA_72,14 +2493541_l,1018733 MM WT,2493541,1,fruit,48.8,MoneyMaker,s_196,s_196,2,e_13_2,6,NA,Sample,452,21111rA_73,21111rA_73,15 +2493633_l,1018728 74630#38.2,2493633,1,fruit,47.2,arlb1-2,s_213,s_213,2,e_14_2,6,NA,Sample,453,21111rA_74,21111rA_74,16 +2493690_l,1016561 Sl10g086190 #21,2493690,1,fruit,51.1,adk1-1,s_220,s_220,2,e_15_2,6,NA,Sample,454,21111rA_75,21111rA_75,17 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,455,21111rA_76,21111rA_76,18 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,456,21111rA_77,21111rA_77,19 +2493591_l,1018727 Sl10g074630 #38,2493591,1,fruit,53,arlb1-1,s_202,s_202,2,e_16_2,6,NA,Sample,457,21111rA_78,21111rA_78,20 +2493593_l,1018727 Sl10g074630 #38,2493593,1,fruit,51.8,arlb1-1,s_204,s_204,2,e_17_2,6,NA,Sample,458,21111rA_79,21111rA_79,21 +2493634_l,1018728 74630#38.2,2493634,1,fruit,53.6,arlb1-2,s_214,s_214,2,e_18_2,6,NA,Sample,459,21111rA_80,21111rA_80,22 +2493592_l,1018727 Sl10g074630 #38,2493592,1,fruit,50.6,arlb1-1,s_203,s_203,2,e_19_2,6,NA,Sample,460,21111rA_81,21111rA_81,23 +2493538_l,1018733 MM WT,2493538,1,fruit,38.1,MoneyMaker,s_193,s_193,2,e_20_2,6,NA,Sample,461,21111rA_82,21111rA_82,24 +2493544_l,1018733 MM WT,2493544,1,fruit,48.9,MoneyMaker,s_199,s_199,2,e_21_2,6,NA,Sample,462,21111rA_83,21111rA_83,25 +2493641_l,1018728 74630#38.2,2493641,1,fruit,50.6,arlb1-2,s_217,s_217,2,e_22_2,6,NA,Sample,463,21111rA_84,21111rA_84,26 +2493564_l,1018732 Sl10g007340#10,2493564,1,fruit,50.8,up1-1,s_201,s_201,2,e_23_2,6,NA,Sample,464,21111rA_85,21111rA_85,27 +2493539_l,1018733 MM WT,2493539,1,fruit,47.1,MoneyMaker,s_194,s_194,2,e_24_2,6,NA,Sample,465,21111rA_86,21111rA_86,28 +2493545_l,1018733 MM WT,2493545,1,fruit,46.8,MoneyMaker,s_200,s_200,2,e_25_2,6,NA,Sample,466,21111rA_87,21111rA_87,29 +2493643_l,1018728 74630#38.2,2493643,1,fruit,53.3,arlb1-2,s_218,s_218,2,e_26_2,6,NA,Sample,467,21111rA_88,21111rA_88,30 +2493543_l,1018733 MM WT,2493543,1,fruit,53.7,MoneyMaker,s_198,s_198,2,e_27_2,6,NA,Sample,468,21111rA_89,21111rA_89,31 +2493640_l,1018728 74630#38.2,2493640,1,fruit,52.1,arlb1-2,s_216,s_216,2,e_28_2,6,NA,Sample,469,21111rA_90,21111rA_90,32 +2493598_l,1018727 Sl10g074630 #38,2493598,1,fruit,46.1,arlb1-1,s_209,s_209,2,e_29_2,6,NA,Sample,470,21111rA_91,21111rA_91,33 +2493594_l,1018727 Sl10g074630 #38,2493594,1,fruit,47.7,arlb1-1,s_205,s_205,2,e_30_2,6,NA,Sample,471,21111rA_92,21111rA_92,34 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,472,21111rA_93,21111rA_93,35 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_0_2,6,NA,Pooled Sample,473,21111rA_94,21111rA_94,36 +NA,NA,NA,NA,fruit,NA,NA,NA,NA,2,e_-1_2,6,NA,blank sample,474,21111rA_95,21111rA_95,37 NA,NA,NA,NA,NA,NA,NA,NA,s_253,other,e_63_other,NA,NA,NA,NA,NA,NA,1 NA,NA,NA,NA,NA,NA,NA,NA,s_254,other,e_49_other,NA,NA,NA,NA,NA,NA,2 NA,NA,NA,NA,NA,NA,NA,NA,s_255,other,e_34_other,NA,NA,NA,NA,NA,NA,3 diff --git a/studies/cmQTL_val1_GH_2020/isa.study.xlsx b/studies/cmQTL_val1_GH_2020/isa.study.xlsx index 3c65526cbef7fd89b22a2c3e6806f6f99f942593..1d80c3ea9dc496b416259b1d42fd383056eea9f3 100644 Binary files a/studies/cmQTL_val1_GH_2020/isa.study.xlsx and b/studies/cmQTL_val1_GH_2020/isa.study.xlsx differ diff --git a/workflows/GC_MS_analysis/210903_primary_analysis_cmQTL_val_1_levene_RxNV.R b/workflows/GC_MS_analysis/210903_primary_analysis_cmQTL_val_1_levene_RxNV.R index e1d3217ecb1f5fd1f79c12eff68941089f27f9fe..aabc89ef016265f01d44f2ece68301e5232d8cb4 100644 --- a/workflows/GC_MS_analysis/210903_primary_analysis_cmQTL_val_1_levene_RxNV.R +++ b/workflows/GC_MS_analysis/210903_primary_analysis_cmQTL_val_1_levene_RxNV.R @@ -1,7 +1,4 @@ -rm(list = ls()) # Set working directory to source file location --------------------------- - -setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) getwd() library(openxlsx) @@ -20,7 +17,7 @@ source <- str_c(current,"/..") cur_date <- str_c(str_replace_all(Sys.Date(),"^.{2}|-","")) -out <- str_c("GC_MS_analysis", sep = "_") +out <- here("runs/GC-MS normalization/") if (file.exists(out)) { cat("The folder already exists") @@ -32,24 +29,24 @@ out_dir <- str_c(current, out, sep = "/") # Data loading ------------------------------------------------------------ -exclude <- read_csv("compound_rts_exclusion.csv") +exclude <- read_csv(here("assays/cmQTL_val1_GH_2020_GC_MS/dataset", "compound_rts_exclusion.csv")) -latest <- str_sort(str_extract(list.files(pattern = "^\\d{6}_normalization$"), - pattern = "^\\d{6}_normalization"), - decreasing = T)[[1]] +#latest <- str_sort(str_extract(list.files(pattern = "^\\d{6}_normalization$"), +# pattern = "^\\d{6}_normalization"), +# decreasing = T)[[1]] -latest_norm <- str_c(current, "/", latest) +#latest_norm <- str_c(current, "/", latest) -setwd(latest_norm) +#setwd(latest_norm) -latest_norm_date <- str_extract(latest, pattern = "^\\d{6}") +#latest_norm_date <- str_extract(latest, pattern = "^\\d{6}") -sam_dat <- read_csv(str_c(latest_norm_date, "_cmQTL_val_1_2_sam_dat_GC.csv")) -met_dat <- read_csv(str_c(latest_norm_date, "_cmQTL_val_1_2_met_dat_GC.csv"), col_types = "ccfdf") %>% +sam_dat <- read_csv(here("runs/GC-MS normalization/cmQTL_val_1_2_sam_dat_GC.csv")) +met_dat <- read_csv(here("runs/GC-MS normalization/cmQTL_val_1_2_met_dat_GC.csv"), col_types = "dcfc") %>% filter(str_detect(Compound_Name,"ribitol", negate = T)) -feat_dat <- read_csv(str_c(latest_norm_date, "_cmQTL_val_1_2_feat_dat_GC.csv"), col_types = "fcffffTiiffidfffcfdddd") +feat_dat <- read_csv(here("runs/GC-MS normalization/cmQTL_val_1_2_feat_dat_GC.csv"), col_types = "fcfffccfidffcfdddd") -setwd(out_dir) +#setwd(out_dir) # Data combination -------------------------------------------------------- @@ -62,8 +59,9 @@ mets <- met_dat$met genotypes <- sam_dat %>% distinct(genotype,.keep_all = T) %>% select(genotype, alias) -GC_classes <- feat_dat %>% - distinct(Compound_Class, Compound_Name, met) +GC_classes <- read.xlsx(here("assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx")) %>% + select(Compound_Class = ChEBI_Ontology_dense, Compound_Name = HMDB_name) %>% + left_join(met_dat) GC_long <- feat_dat %>% left_join(met_dat) %>% diff --git a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R index 033dfcf79a7ede6c299cd44b58bea53f7afc2648..d72b5f081ab28c6faf3a08cf4dc8c542e4021266 100644 --- a/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R +++ b/workflows/GC_MS_normalization/210927_primary_normalization_with_split.R @@ -1,5 +1,3 @@ -rm(list = ls()) - library(openxlsx) library(tidyverse) library(car) @@ -25,7 +23,7 @@ if (file.exists(out)) { } else { dir.create(out) } -setwd(here())# Not recommended but convenient in Rstudio to start from root +#setwd(here())# Not recommended but convenient in Rstudio to start from root # Data loading ------------------------------------------------------------ @@ -65,7 +63,7 @@ rt_mean <- area %>% summarise(RT_mean = mean(rt, na.rm = T)) metdat_GC_class <- readxl::read_xlsx(here("assays/cmQTL_val1_GH_2020_GC_MS/dataset/MAF_GC_MS.xlsx")) %>% - select(component = Xcal_name_xreport, Compound_Name = PubChem_Name_mapped)%>% + select(component = Xcal_name_xreport, Compound_Name = HMDB_name)%>% left_join(rt_mean) %>% filter(!is.na(component)) %>% arrange(Compound_Name, RT_mean) %>%