The advent of mass spectrometry based analytical technologies coupled with multivariate statistical methods offers tremendous new opportunities for understanding the pharmacokinetics of multicomponent herbal medicines. In recent years, Jia’s group proposed a polyPK strategy, in a few review papers (Science 2015, Current Drug Metabolism 2010, Evidence-Based Complementary and Alternative Medicine 2013), to characterize the concentration-time profile and the metabolic response profile of multicomponent drugs, using an integrated phytochemical and metabolomics approach. The brand new strategy has been successfully applied in examining the complex pharmacokinetics and pharmacodynamics profiles of tea (Journal of Proteome Research 2012) and Huangqi decoction (Clinical Pharmacology & Therapeutics 2016). This package is the first implementation of the polyPK strategy with 10 easy-to-use functions. The absorbed drug constitutes, the downstream metabolites of the drug constituents and the endogenous metabolites impacted by them can be identified. The association of different types of compounds and their alterations along time can be illustrated by various figures and tables. The representative PK parameters of all compounds can be calculated.
10 functions of the package of polyPK: DataPre,GetDiffData,GetEndo,GetAbso,GetSecdAbso,PKs,Simi,ScatPlot,HeatMap,CorrPlot
DataPrePreprocess the input data. Variables with a lot of zeros and outliers may be removed. Missing values may be imputed and filled by various methods. Data may be transformed by logarithm transformation.
library(polyPK)data("postData")
pred_post<-polyPK::DataPre(tes=postData,mv="mean",rz=80,multiple=0.1,sv=TRUE,log=FALSE,filepath=getwd())An example of preprocessed post-dose dataset:
pred_post[c(1:10),c(1:10)]## Name ID m.z RT.min. X1.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 1
## 3 timepoints(h) <NA> <NA> 0.083
## 4 isoliquiritigenin HMDB30808 255.0682 1.4637000 1.370141e+03
## 5 hyocholic acid inx0005 407.2801 3.2258500 2.784204e+02
## 6 octanoyl-rac-glycerol inx0001 219.1489 3.3205667 3.720998e+03
## 7 oxalosuccinic acid HMDB03974 191.0185 0.6874667 2.020981e+03
## 8 palmitic amide HMDB12273 256.2634 6.9251500 2.002083e+05
## 9 phenylalanine HMDB00159 218.0000 13.1564258 1.540889e+06
## 10 stearidonic acid HMDB06547 275.2011 4.0438833 2.247636e+01
## X1.2 X1.3 X1.4 X1.5 X1.6
## 1 1 1 1 1 2
## 2 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083
## 4 3.178774e+03 5.442983e+02 1.379580e+03 3.237247e+03 7.937158e+02
## 5 2.784204e+02 2.784204e+02 2.784204e+02 2.784204e+02 2.784204e+02
## 6 1.617713e+03 2.905334e+03 4.732409e+03 3.777234e+03 1.904859e+03
## 7 1.814765e+03 2.009507e+03 2.375203e+03 2.492505e+03 6.724538e+02
## 8 1.655981e+05 3.131862e+05 2.078951e+05 1.800302e+05 6.973914e+05
## 9 1.119705e+06 1.310229e+06 1.475237e+06 1.878999e+06 1.100194e+06
## 10 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01SimiA function which can get the similar metabolites of two datas.Especially the similar metabolites between drug and pre-dose metabolites.
data("preData")
data("drugData")
Simi(data1<-preData,data2<-drugData,filepath=getwd())## $`repetitive rates in data1`
## [1] 0.1
##
## $`repetitive rates in data2`
## [1] 0.3333333
##
## $`similar metabolites`
## data1[-c(1:3), 2]
## [1,] "inx0001"GetDiffDataA function to get all the differential compounds between the pre-dose and every post-dose datasets:
data("preData")
data("postData")
data("design")
data("simidata")
dif<-GetDiffData(preData,postData,simidata,mv="mean",rz=80,multiple=0.1,sv=TRUE,log=FALSE,t="Ttest",r.adj="fdr",filepath=getwd(),design=design)
#'An example of the differential compounds, with preprocessed data:
prepoA<-dif$A[c(1:12),c(1:7)]
as.data.frame(prepoA)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 15 octanoyl-rac-glycerol inx0001 219.1401 3.5638000 4180.3304
## 21 n-dodecanoic acid HMDB00638 199.1693 5.2730000 141903.8371
## 31 3-hydroxybutyric acid HMDB00357 103.0400 0.6600000 18175.8722
## 4 taurine HMDB00251 124.0100 0.6800000 54652.4522
## 5 phenylpyruvic acid HMDB00205 165.0545 3.5218833 12599.6705
## 6 hyocholic acid inx0005 407.2801 3.2258500 <NA>
## 7 isoliquiritigenin HMDB30808 255.0682 1.4637000 <NA>
## 8 stearidonic acid HMDB06547 275.2011 4.0438833 <NA>
## 9 2-aminobutyric acid HMDB00452 104.0545 0.7084167 <NA>
## X0.2 X0.3
## 1 1 1
## 2 0 0
## 3 0 0
## 15 5075.2366 4765.7406
## 21 142425.9489 59180.5145
## 31 14711.6639 11916.5011
## 4 58416.8343 60813.0134
## 5 13562.6711 20083.7873
## 6 <NA> <NA>
## 7 <NA> <NA>
## 8 <NA> <NA>
## 9 <NA> <NA>An example of the differential compounds, with original data:
orgA<-dif$A_pre[c(1:12),c(1:7)]
as.data.frame(orgA)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 15 phenylpyruvic acid HMDB00205 165.0545212 3.521883333 12599.67047
## 21 taurine HMDB00251 124.01 0.68 54652.45217
## 31 3-hydroxybutyric acid HMDB00357 103.04 0.66 18175.87221
## 4 n-dodecanoic acid HMDB00638 199.1693 5.273 141903.8371
## 5 octanoyl-rac-glycerol inx0001 219.1401489 3.5638 4180.330371
## 6 hyocholic acid inx0005 407.2801088 3.22585 <NA>
## 7 isoliquiritigenin HMDB30808 255.0681916 1.4637 <NA>
## 8 stearidonic acid HMDB06547 275.2010927 4.043883333 <NA>
## 9 2-aminobutyric acid HMDB00452 104.0544716 0.708416667 <NA>
## X0.2 X0.3
## 1 1 1
## 2 0 0
## 3 0 0
## 15 13562.67108 20083.78726
## 21 58416.83432 60813.01343
## 31 14711.66391 11916.50106
## 4 142425.9489 59180.51449
## 5 5075.236614 4765.740625
## 6 <NA> <NA>
## 7 <NA> <NA>
## 8 <NA> <NA>
## 9 <NA> <NA>The p values:
p<-dif$p
p## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.02612277 0.46625184 0.059124442 0.0171618488 6.277746e-05
## [2,] 0.21600723 0.08936120 0.116288148 0.2767443294 3.257084e-01
## [3,] 0.55931404 0.62797776 0.754002236 0.9951415474 2.926128e-01
## [4,] 0.90010481 0.86732615 0.124180790 0.0124306102 6.269413e-02
## [5,] 0.27534667 0.09259060 0.114830950 0.1015186587 1.201289e-01
## [6,] 0.83651369 0.82068000 0.371571328 0.9196653728 5.379117e-01
## [7,] 0.05934515 0.01212962 0.002326595 0.0008524079 2.120064e-04
## [,6] [,7] [,8] [,9]
## [1,] 0.0001156508 0.0001227209 0.0006174414 1.934193e-05
## [2,] 0.2112745475 0.5267109128 0.7750469254 1.537414e-02
## [3,] 0.3359581296 0.3751420887 0.1916954009 3.250817e-02
## [4,] 0.5198512612 0.0024744481 0.0045402806 4.330134e-03
## [5,] 0.0002520865 0.5068921065 0.8579179695 8.266721e-01
## [6,] 0.1647501303 0.7312084247 0.5184174149 7.630634e-04
## [7,] 0.0001290038 0.0143945068 0.0309441731 1.203254e-01The adjusted p values:
padj<-dif$p_adj
padj## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 0.08228671 0.65275258 0.15578102 0.05690508 0.001625448 0.001625448
## [2,] 0.36779610 0.21604474 0.23689069 0.44704853 0.500478690 0.367796101
## [3,] 0.69091734 0.76081921 0.87966928 0.99514155 0.460865118 0.503937194
## [4,] 0.92961644 0.91069246 0.23707242 0.04894553 0.157989205 0.677199745
## [5,] 0.44704853 0.21604474 0.23689069 0.22841698 0.236890686 0.002268779
## [6,] 0.90862694 0.90862694 0.53713526 0.93449869 0.677768739 0.305272300
## [7,] 0.15578102 0.04894553 0.01299085 0.00537017 0.002226067 0.001625448
## [,7] [,8] [,9]
## [1,] 0.001625448 0.004862351 0.001218541
## [2,] 0.677199745 0.887781024 0.053809475
## [3,] 0.537135263 0.345051722 0.093091570
## [4,] 0.012990853 0.020431263 0.020431263
## [5,] 0.677199745 0.910692456 0.908626938
## [6,] 0.869172278 0.677199745 0.005341444
## [7,] 0.053344349 0.092832519 0.236890686GetEndoA function to get the altered endogenous metabolites by similarity analysis on the list of differential compounds and the list of pre-dose compounds：
data("preData")
data("A")
data("design")
data("simidata")
GetEndo(preData,A,simidata,sim=80,filepath=getwd(),design=design)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 14 octanoyl-rac-glycerol inx0001 219.1401 3.5638000 4180.330
## 12 hippuric acid HMDB00714 178.0503 0.7566000 1503.207
## 13 hexadecanedioic acid HMDB00672 285.2062 4.0334167 3250.311
## 21 n-dodecanoic acid HMDB00638 199.1693 5.2730000 141903.837
## 31 3-hydroxybutyric acid HMDB00357 103.0400 0.6600000 18175.872
## 4 taurine HMDB00251 124.0100 0.6800000 54652.452
## 5 phenylpyruvic acid HMDB00205 165.0545 3.5218833 12599.670
## X0.2 X0.3 X0.4 X0.5 X0.6 X0.7
## 1 1 1 1 1 2 2
## 2 0 0 0 0 0 0
## 3 0 0 0 0 0 0
## 14 5075.237 4765.7406 4081.1987 2735.835 4993.6567 4433.1691
## 12 8011.543 2280.2458 5714.8831 7332.153 3401.4469 7810.1283
## 13 2808.426 264.2712 583.6932 2367.337 827.6251 328.7123
## 21 142425.949 59180.5145 51617.3287 46397.367 144256.4372 28979.3290
## 31 14711.664 11916.5011 4837.1843 10554.832 6304.4677 3049.0139
## 4 58416.834 60813.0134 64769.4094 64769.409 36992.0058 59748.2733
## 5 13562.671 20083.7873 19057.1646 19298.528 16289.8042 19507.4954
## X0.8 X0.9 X0.10 X1.1 X1.2
## 1 2 2 2 1 1
## 2 0 0 0 1 1
## 3 0 0 0 0.083 0.083
## 14 4149.5551 3543.962 3309.242 3.720998e+03 1.617713e+03
## 12 2085.4607 10201.423 10201.423 <NA> <NA>
## 13 986.9264 3250.311 3219.459 <NA> <NA>
## 21 72072.4159 96966.887 202042.030 7.605930e+04 1.469626e+05
## 31 5876.3078 12417.050 10591.569 2.328958e+04 2.097504e+04
## 4 54113.2992 50096.305 54601.927 4.706105e+04 6.159389e+04
## 5 21049.4087 17280.879 21919.076 1.044584e+04 1.422142e+04
## X1.3 X1.4 X1.5 X1.6 X1.7
## 1 1 1 1 2 2
## 2 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083
## 14 2.905334e+03 4.732409e+03 3.777234e+03 1.904859e+03 2.830200e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 8.931413e+04 5.503614e+04 5.126085e+04 1.420261e+05 5.738844e+04
## 31 1.333990e+04 5.702339e+03 1.273751e+04 6.457741e+03 4.600448e+03
## 4 6.463091e+04 6.946875e+04 6.031007e+04 3.541851e+04 5.317371e+04
## 5 2.242246e+04 1.792318e+04 1.352738e+04 1.408044e+04 1.490617e+04
## X1.8 X1.9 X1.10 X2.1 X2.2
## 1 2 2 2 1 1
## 2 1 1 1 2 2
## 3 0.083 0.083 0.083 0.25 0.25
## 14 2.992664e+03 2.832788e+03 4.350362e+03 3.033735e+03 3.858627e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 1.063669e+05 1.050993e+05 1.293370e+05 7.231874e+04 1.469626e+05
## 31 1.085076e+04 1.684745e+04 1.177731e+04 1.948900e+04 1.995786e+04
## 4 4.892039e+04 5.108606e+04 5.878497e+04 5.677723e+04 6.186181e+04
## 5 1.616860e+04 1.102098e+04 1.640514e+04 1.288955e+04 1.434161e+04
## X2.3 X2.4 X2.5 X2.6 X2.7
## 1 1 1 1 2 2
## 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25
## 14 3.880638e+03 4.293698e+03 2.724455e+03 4.105260e+03 4.403498e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 8.280487e+04 6.358682e+04 4.967099e+04 1.469626e+05 4.431479e+04
## 31 1.364561e+04 7.308365e+03 1.763203e+04 8.910625e+03 4.922363e+03
## 4 6.484992e+04 6.592919e+04 5.467160e+04 3.877003e+04 5.755359e+04
## 5 1.958049e+04 1.534140e+04 1.375062e+04 1.342531e+04 1.619240e+04
## X2.8 X2.9 X2.10 X3.1 X3.2
## 1 2 2 2 1 1
## 2 2 2 2 3 3
## 3 0.25 0.25 0.25 0.5 0.5
## 14 2.925096e+03 4.931640e+03 4.606038e+03 4.211090e+03 2.375966e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 9.295671e+04 1.021819e+05 1.469626e+05 4.769324e+04 8.845760e+04
## 31 1.414883e+04 1.854192e+04 1.393188e+04 1.974212e+04 2.037162e+04
## 4 4.713009e+04 4.952651e+04 5.339489e+04 4.992021e+04 6.241529e+04
## 5 1.245178e+04 1.338572e+04 1.572960e+04 9.024338e+03 1.059318e+04
## X3.3 X3.4 X3.5 X3.6 X3.7
## 1 1 1 1 2 2
## 2 3 3 3 3 3
## 3 0.5 0.5 0.5 0.5 0.5
## 14 2.337628e+03 3.525279e+03 3.716061e+03 3.870560e+03 3.280670e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 4.537689e+04 4.738112e+04 3.414156e+04 8.604576e+04 4.634118e+04
## 31 1.588789e+04 6.761843e+03 1.766571e+04 1.007156e+04 4.981084e+03
## 4 5.222740e+04 6.611711e+04 5.776128e+04 3.235281e+04 5.803822e+04
## 5 1.648677e+04 1.550028e+04 1.350743e+04 1.184193e+04 1.514302e+04
## X3.8 X3.9 X3.10 X4.1 X4.2
## 1 2 2 2 1 1
## 2 3 3 3 4 4
## 3 0.5 0.5 0.5 1 1
## 14 2.743306e+03 3.393244e+03 4.839369e+03 2646.1411 3448.7697
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 7.838628e+04 7.489274e+04 1.141746e+05 33146.1590 48937.3308
## 31 1.447867e+04 1.552779e+04 1.036542e+04 14054.8494 15689.7455
## 4 4.877033e+04 4.475100e+04 5.000915e+04 57140.3900 62744.8885
## 5 1.555570e+04 1.289372e+04 1.537515e+04 11066.0933 13289.9653
## X4.3 X4.4 X4.5 X4.6 X4.7
## 1 1 1 1 2 2
## 2 4 4 4 4 4
## 3 1 1 1 1 1
## 14 2674.3427 3280.8034 4711.6220 3008.1355 4086.1531
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 30312.3939 33495.2690 23426.9284 44921.5102 28612.4767
## 31 14189.6975 7565.3947 18590.6536 9075.0677 7047.9361
## 4 68100.3304 69966.4003 54660.5149 36808.5758 52146.4470
## 5 15061.9170 17281.8554 11946.4339 12447.5308 11634.6515
## X4.8 X4.9 X4.10 X5.1 X5.2
## 1 2 2 2 1 1
## 2 4 4 4 5 5
## 3 1 1 1 2 2
## 14 3065.9686 3.318351e+03 2673.8852 3625.4119 2496.3978
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 77882.3440 5.736015e+04 48629.5463 45273.1698 63106.2309
## 31 18401.5305 1.394928e+04 14275.5131 13608.0650 14624.1756
## 4 53497.0486 4.773151e+04 52054.0387 51216.7729 58310.0320
## 5 13193.0917 1.352302e+04 13724.5891 9336.2797 10688.9841
## X5.3 X5.4 X5.5 X5.6 X5.7
## 1 1 1 1 2 2
## 2 5 5 5 5 5
## 3 2 2 2 2 2
## 14 1757.0399 2564.2173 2805.7129 1153.0243 2927.9869
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 71162.6265 44618.7281 39864.8524 68781.1399 49358.2478
## 31 17375.0748 8023.0523 15917.8028 11289.1375 6582.2637
## 4 62193.3641 66204.7945 54095.1389 27649.2229 62424.6592
## 5 15221.4307 15869.2806 12256.3657 9960.2915 13835.1103
## X5.8 X5.9 X5.10 X6.1 X6.2
## 1 2 2 2 1 1
## 2 5 5 5 6 6
## 3 2 2 2 4 4
## 14 2.840386e+03 2265.3794 2127.2873 2.223131e+03 3.315628e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 8.212366e+04 55218.3199 80796.1338 1.014137e+05 1.469626e+05
## 31 1.462658e+04 11938.2909 14961.5945 2.328958e+04 2.328958e+04
## 4 5.260916e+04 49785.7178 47439.7803 4.965634e+04 5.907598e+04
## 5 1.126301e+04 11942.4501 13386.1634 1.033427e+04 1.154178e+04
## X6.3 X6.4 X6.5 X6.6 X6.7
## 1 1 1 1 2 2
## 2 6 6 6 6 6
## 3 4 4 4 4 4
## 14 1.634174e+03 2.398416e+03 3.421965e+03 2.429446e+03 2661.69124
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 9.524910e+04 1.026721e+05 6.433207e+04 1.053721e+05 91122.34592
## 31 2.236307e+04 1.722697e+04 1.769843e+04 2.216890e+04 7365.18413
## 4 5.067346e+04 6.203562e+04 6.184344e+04 2.607769e+04 52979.62924
## 5 1.554430e+04 1.414057e+04 1.397293e+04 9.197782e+03 12655.08525
## X6.8 X6.9 X6.10 X7.1 X7.2
## 1 2 2 2 1 1
## 2 6 6 6 7 7
## 3 4 4 4 6 6
## 14 2.496147e+03 3.292361e+03 2.549347e+03 2569.5941 2091.5383
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 1.242132e+05 1.382707e+05 1.469626e+05 22538.8198 33672.2500
## 31 1.844305e+04 2.328958e+04 2.228411e+04 9717.0654 8860.1942
## 4 4.764263e+04 4.554991e+04 4.121457e+04 50806.3970 63487.2146
## 5 1.148499e+04 1.292732e+04 9.334460e+03 13709.8587 13031.8151
## X7.3 X7.4 X7.5 X7.6 X7.7
## 1 1 1 1 2 2
## 2 7 7 7 7 7
## 3 6 6 6 6 6
## 14 3224.4716 1069.9343 2833.4270 3281.9023 2852.8213
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 21908.8215 20041.1797 17756.9783 15873.4543 27423.6067
## 31 11688.1072 4773.2167 10027.3593 5519.2398 2817.7406
## 4 57635.5798 69835.3532 62094.5497 34354.6655 56728.9915
## 5 16420.2844 19829.8223 15156.4648 15314.1648 15039.9007
## X7.8 X7.9 X7.10 X8.1 X8.2
## 1 2 2 2 1 1
## 2 7 7 7 8 8
## 3 6 6 6 8 8
## 14 3.122827e+03 2533.6538 1949.3774 4176.2008 2620.2380
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 3.838789e+04 23277.3524 26501.2144 26811.1937 69407.9927
## 31 1.202016e+04 12236.8362 8376.5918 12885.1370 16843.4817
## 4 4.942499e+04 45504.8476 54776.2816 49162.7414 59614.9149
## 5 1.145925e+04 13272.9344 14194.5551 14794.4984 14420.8686
## X8.3 X8.4 X8.5 X8.6 X8.7
## 1 1 1 1 2 2
## 2 8 8 8 8 8
## 3 8 8 8 8 8
## 14 2913.3486 2156.3241 2800.5507 1448.1588 3355.5500
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 24886.6558 22379.2699 18564.0535 19135.7185 34740.0489
## 31 16287.8127 9746.7944 8054.4287 4918.1340 3816.5593
## 4 54975.2092 69752.0873 60342.5721 32318.3457 56005.7351
## 5 13634.0621 17743.6931 13723.3396 14348.5309 17725.6065
## X8.8 X8.9 X8.10 X9.1 X9.2
## 1 2 2 2 1 1
## 2 8 8 8 9 9
## 3 8 8 8 12 12
## 14 3259.7042 2178.2957 1612.6917 3104.3817 2302.8018
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 40620.5428 27205.8960 35211.7355 27515.0727 42167.8269
## 31 8923.5228 11139.6164 9499.2554 10052.0863 10084.5435
## 4 49548.9635 44694.4717 55458.7038 37258.5278 47252.7818
## 5 16274.9108 12681.7156 17851.4361 12396.2625 12877.3790
## X9.3 X9.4 X9.5 X9.6 X9.7
## 1 1 1 1 2 2
## 2 9 9 9 9 9
## 3 12 12 12 12 12
## 14 1669.0013 1943.9478 2509.6361 2594.4257 2417.0276
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 22802.5729 28154.5848 23661.2598 40176.8066 27525.2985
## 31 8019.7218 9208.8476 12075.6040 8632.2730 10279.8178
## 4 50310.1439 50824.7802 33861.4708 21824.1567 41622.4399
## 5 16021.4916 16682.1509 11545.3308 13057.4590 18491.8933
## X9.8 X9.9 X9.10 X10.1 X10.2
## 1 2 2 2 1 1
## 2 9 9 9 10 10
## 3 12 12 12 15 15
## 14 2823.3098 2427.6707 2323.4552 4.931640e+03 2.580926e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 55318.9912 19773.6083 26281.2463 3.803529e+04 9.348853e+04
## 31 10249.8927 7175.5229 9133.0329 8.955081e+03 9.971469e+03
## 4 44041.3622 41389.4134 38642.8130 4.533420e+04 5.333024e+04
## 5 20000.7230 18798.8763 18197.9797 1.612145e+04 1.617697e+04
## X10.3 X10.4 X10.5 X10.6 X10.7
## 1 1 1 1 2 2
## 2 10 10 10 10 10
## 3 15 15 15 15 15
## 14 2.957264e+03 4.931640e+03 4.931640e+03 4.106450e+03 3.791994e+03
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 3.387132e+04 4.706431e+04 2.671882e+04 2.054585e+04 4.026237e+04
## 31 1.273101e+04 1.133352e+04 6.630398e+03 3.929941e+03 8.896966e+03
## 4 4.084886e+04 5.327472e+04 4.432993e+04 2.456119e+04 4.840988e+04
## 5 1.691849e+04 1.575817e+04 1.576261e+04 1.643388e+04 2.215846e+04
## X10.8 X10.9 X10.10 X11.1 X11.2
## 1 2 2 2 1 1
## 2 10 10 10 11 11
## 3 15 15 15 24 24
## 14 2.394015e+03 2.995298e+03 4.410297e+03 3786.8261 2450.1092
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 3.771719e+04 4.048115e+04 6.071908e+04 75174.0072 142272.1077
## 31 8.235472e+03 1.032865e+04 9.014239e+03 23289.5757 22099.4459
## 4 4.149762e+04 3.751521e+04 3.916361e+04 39974.8729 52580.9254
## 5 2.004001e+04 1.785776e+04 2.199665e+04 11325.3370 14728.8059
## X11.3 X11.4 X11.5 X11.6 X11.7
## 1 1 1 1 2 2
## 2 11 11 11 11 11
## 3 24 24 24 24 24
## 14 3631.7646 3694.9784 4251.2509 3846.2226 3426.6954
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 45916.3893 34609.0358 39799.0796 61092.9545 31213.7897
## 31 12292.4884 8308.3776 9714.6148 6527.4914 8221.9684
## 4 46465.7693 57928.3884 49312.1700 26414.1202 37791.4269
## 5 16736.9962 17799.8468 17262.3943 16750.8836 11562.0545
## X11.8 X11.9 X11.10 X12.1 X12.2
## 1 2 2 2 1 1
## 2 11 11 11 12 12
## 3 24 24 24 30 30
## 14 4294.9415 3579.1423 2801.7475 2.412480e+03 3014.9726
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 62966.3761 81113.8716 146962.5562 2.444179e+04 22656.5926
## 31 7181.3820 14319.5488 9286.2912 5.353311e+03 6072.4709
## 4 40129.3740 46762.5877 42765.1208 4.232468e+04 47900.9869
## 5 17690.5999 14200.5060 22494.7335 1.386842e+04 16167.4516
## X12.3 X12.4 X12.5 X12.6 X12.7
## 1 1 1 1 2 2
## 2 12 12 12 12 12
## 3 30 30 30 30 30
## 14 2499.3959 3184.6637 3447.7610 2943.2554 3266.5058
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 26310.1731 19663.2144 17304.5485 25439.9582 20441.0797
## 31 11391.4062 7396.7657 7203.8244 5097.7827 4870.6579
## 4 55117.6536 60017.8909 49888.4775 27109.7985 40987.6165
## 5 16476.0118 20502.5317 19034.4862 17630.8662 23133.3750
## X12.8 X12.9 X12.10 X13.1 X13.2
## 1 2 2 2 1 1
## 2 12 12 12 13 13
## 3 30 30 30 36 36
## 14 2394.0848 3662.6803 2141.3351 2041.6406 4122.3177
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 17874.0162 22993.7204 97347.6495 34308.4041 36726.4892
## 31 3337.9556 5590.1410 5994.4761 4716.3373 7950.8900
## 4 38833.7715 46435.8170 38336.9415 39936.8587 51126.5511
## 5 22709.3805 21484.3154 23133.3750 18401.1806 21490.9623
## X13.3 X13.4 X13.5 X13.6 X13.7
## 1 1 1 1 2 2
## 2 13 13 13 13 13
## 3 36 36 36 36 36
## 14 3089.5949 2128.9795 1803.5259 1980.3018 1663.6182
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 40972.7242 25053.4760 18872.9087 17986.2127 17973.6294
## 31 10058.5237 9082.4223 7206.7749 3402.9196 3040.9171
## 4 57031.2540 59274.6392 49070.7728 23060.6726 37083.7883
## 5 20144.4416 21354.3859 19556.9586 14602.3514 22018.3589
## X13.8 X13.9 X13.10 X14.1 X14.2
## 1 2 2 2 1 1
## 2 13 13 13 14 14
## 3 36 36 36 48 48
## 14 3.140954e+03 3716.8585 3804.5102 1852.6829 2982.4361
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 2.634719e+04 16413.0403 67902.0059 38769.8847 67228.2332
## 31 4.572209e+03 3943.9430 8364.9650 9038.7290 9639.1306
## 4 3.758764e+04 38408.3504 42264.3040 45881.4797 48798.8977
## 5 2.037819e+04 17414.1017 20419.7985 20173.8645 16305.4559
## X14.3 X14.4 X14.5 X14.6 X14.7
## 1 1 1 1 2 2
## 2 14 14 14 14 14
## 3 48 48 48 48 48
## 14 2776.7269 1446.9467 2898.6008 2577.6334 1728.8296
## 12 <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA>
## 21 36668.7583 50382.2158 36389.7581 65603.2122 30331.9468
## 31 9332.6231 7580.8794 13940.9068 6885.6864 4835.5802
## 4 53759.4183 51713.7508 41652.1014 26645.2014 43304.8501
## 5 20309.8359 15698.9636 12967.0660 15821.2225 15643.2164
## X14.8 X14.9 X14.10
## 1 2 2 2
## 2 14 14 14
## 3 48 48 48
## 14 3.392003e+03 2340.2763 3461.0021
## 12 <NA> <NA> <NA>
## 13 <NA> <NA> <NA>
## 21 5.168826e+04 65832.6529 78992.6889
## 31 4.889092e+03 10104.7391 9116.5366
## 4 4.003441e+04 42366.3993 35571.1420
## 5 1.482644e+04 16675.6523 15238.7700GetAbsoA function to get the absorbed drug constitutes by similarity analysis on the list of differential compounds and the list of drug constitutes:
GetAbso(drugData, A, simidata,sim = 80, filepath=getwd(),design = design)## Name ID m.z RT.min. X0.1 X0.2
## 1 gender <NA> <NA> 1 1
## 2 group <NA> <NA> 0 0
## 3 timepoints(h) <NA> <NA> 0 0
## 14 octanoyl-rac-glycerol inx0001 219.1401 3.5638000 4180.330 5075.237
## X0.3 X0.4 X0.5 X0.6 X0.7 X0.8
## 1 1 1 1 2 2 2
## 2 0 0 0 0 0 0
## 3 0 0 0 0 0 0
## 14 4765.7406 4081.1987 2735.835 4993.6567 4433.1691 4149.5551
## X0.9 X0.10 X1.1 X1.2 X1.3
## 1 2 2 1 1 1
## 2 0 0 1 1 1
## 3 0 0 0.083 0.083 0.083
## 14 3543.962 3309.242 3.720998e+03 1.617713e+03 2.905334e+03
## X1.4 X1.5 X1.6 X1.7 X1.8
## 1 1 1 2 2 2
## 2 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083
## 14 4.732409e+03 3.777234e+03 1.904859e+03 2.830200e+03 2.992664e+03
## X1.9 X1.10 X2.1 X2.2 X2.3
## 1 2 2 1 1 1
## 2 1 1 2 2 2
## 3 0.083 0.083 0.25 0.25 0.25
## 14 2.832788e+03 4.350362e+03 3.033735e+03 3.858627e+03 3.880638e+03
## X2.4 X2.5 X2.6 X2.7 X2.8
## 1 1 1 2 2 2
## 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25
## 14 4.293698e+03 2.724455e+03 4.105260e+03 4.403498e+03 2.925096e+03
## X2.9 X2.10 X3.1 X3.2 X3.3
## 1 2 2 1 1 1
## 2 2 2 3 3 3
## 3 0.25 0.25 0.5 0.5 0.5
## 14 4.931640e+03 4.606038e+03 4.211090e+03 2.375966e+03 2.337628e+03
## X3.4 X3.5 X3.6 X3.7 X3.8
## 1 1 1 2 2 2
## 2 3 3 3 3 3
## 3 0.5 0.5 0.5 0.5 0.5
## 14 3.525279e+03 3.716061e+03 3.870560e+03 3.280670e+03 2.743306e+03
## X3.9 X3.10 X4.1 X4.2 X4.3
## 1 2 2 1 1 1
## 2 3 3 4 4 4
## 3 0.5 0.5 1 1 1
## 14 3.393244e+03 4.839369e+03 2646.1411 3448.7697 2674.3427
## X4.4 X4.5 X4.6 X4.7 X4.8
## 1 1 1 2 2 2
## 2 4 4 4 4 4
## 3 1 1 1 1 1
## 14 3280.8034 4711.6220 3008.1355 4086.1531 3065.9686
## X4.9 X4.10 X5.1 X5.2 X5.3
## 1 2 2 1 1 1
## 2 4 4 5 5 5
## 3 1 1 2 2 2
## 14 3.318351e+03 2673.8852 3625.4119 2496.3978 1757.0399
## X5.4 X5.5 X5.6 X5.7 X5.8
## 1 1 1 2 2 2
## 2 5 5 5 5 5
## 3 2 2 2 2 2
## 14 2564.2173 2805.7129 1153.0243 2927.9869 2.840386e+03
## X5.9 X5.10 X6.1 X6.2 X6.3
## 1 2 2 1 1 1
## 2 5 5 6 6 6
## 3 2 2 4 4 4
## 14 2265.3794 2127.2873 2.223131e+03 3.315628e+03 1.634174e+03
## X6.4 X6.5 X6.6 X6.7 X6.8
## 1 1 1 2 2 2
## 2 6 6 6 6 6
## 3 4 4 4 4 4
## 14 2.398416e+03 3.421965e+03 2.429446e+03 2661.69124 2.496147e+03
## X6.9 X6.10 X7.1 X7.2 X7.3
## 1 2 2 1 1 1
## 2 6 6 7 7 7
## 3 4 4 6 6 6
## 14 3.292361e+03 2.549347e+03 2569.5941 2091.5383 3224.4716
## X7.4 X7.5 X7.6 X7.7 X7.8
## 1 1 1 2 2 2
## 2 7 7 7 7 7
## 3 6 6 6 6 6
## 14 1069.9343 2833.4270 3281.9023 2852.8213 3.122827e+03
## X7.9 X7.10 X8.1 X8.2 X8.3
## 1 2 2 1 1 1
## 2 7 7 8 8 8
## 3 6 6 8 8 8
## 14 2533.6538 1949.3774 4176.2008 2620.2380 2913.3486
## X8.4 X8.5 X8.6 X8.7 X8.8
## 1 1 1 2 2 2
## 2 8 8 8 8 8
## 3 8 8 8 8 8
## 14 2156.3241 2800.5507 1448.1588 3355.5500 3259.7042
## X8.9 X8.10 X9.1 X9.2 X9.3
## 1 2 2 1 1 1
## 2 8 8 9 9 9
## 3 8 8 12 12 12
## 14 2178.2957 1612.6917 3104.3817 2302.8018 1669.0013
## X9.4 X9.5 X9.6 X9.7 X9.8
## 1 1 1 2 2 2
## 2 9 9 9 9 9
## 3 12 12 12 12 12
## 14 1943.9478 2509.6361 2594.4257 2417.0276 2823.3098
## X9.9 X9.10 X10.1 X10.2 X10.3
## 1 2 2 1 1 1
## 2 9 9 10 10 10
## 3 12 12 15 15 15
## 14 2427.6707 2323.4552 4.931640e+03 2.580926e+03 2.957264e+03
## X10.4 X10.5 X10.6 X10.7 X10.8
## 1 1 1 2 2 2
## 2 10 10 10 10 10
## 3 15 15 15 15 15
## 14 4.931640e+03 4.931640e+03 4.106450e+03 3.791994e+03 2.394015e+03
## X10.9 X10.10 X11.1 X11.2 X11.3
## 1 2 2 1 1 1
## 2 10 10 11 11 11
## 3 15 15 24 24 24
## 14 2.995298e+03 4.410297e+03 3786.8261 2450.1092 3631.7646
## X11.4 X11.5 X11.6 X11.7 X11.8
## 1 1 1 2 2 2
## 2 11 11 11 11 11
## 3 24 24 24 24 24
## 14 3694.9784 4251.2509 3846.2226 3426.6954 4294.9415
## X11.9 X11.10 X12.1 X12.2 X12.3
## 1 2 2 1 1 1
## 2 11 11 12 12 12
## 3 24 24 30 30 30
## 14 3579.1423 2801.7475 2.412480e+03 3014.9726 2499.3959
## X12.4 X12.5 X12.6 X12.7 X12.8
## 1 1 1 2 2 2
## 2 12 12 12 12 12
## 3 30 30 30 30 30
## 14 3184.6637 3447.7610 2943.2554 3266.5058 2394.0848
## X12.9 X12.10 X13.1 X13.2 X13.3
## 1 2 2 1 1 1
## 2 12 12 13 13 13
## 3 30 30 36 36 36
## 14 3662.6803 2141.3351 2041.6406 4122.3177 3089.5949
## X13.4 X13.5 X13.6 X13.7 X13.8
## 1 1 1 2 2 2
## 2 13 13 13 13 13
## 3 36 36 36 36 36
## 14 2128.9795 1803.5259 1980.3018 1663.6182 3.140954e+03
## X13.9 X13.10 X14.1 X14.2 X14.3
## 1 2 2 1 1 1
## 2 13 13 14 14 14
## 3 36 36 48 48 48
## 14 3716.8585 3804.5102 1852.6829 2982.4361 2776.7269
## X14.4 X14.5 X14.6 X14.7 X14.8
## 1 1 1 2 2 2
## 2 14 14 14 14 14
## 3 48 48 48 48 48
## 14 1446.9467 2898.6008 2577.6334 1728.8296 3.392003e+03
## X14.9 X14.10
## 1 2 2
## 2 14 14
## 3 48 48
## 14 2340.2763 3461.0021GetSecdAbsoA function to get secondary metabolites of the absorbed drug constitutes:
GetSecdAbso(A,B,C,simidata,sim=80,filepath=getwd(),design)## Name ID m.z RT.min. X0.1 X0.2 X0.3 X0.4
## 1 gender <NA> <NA> 1 1 1 1
## 2 group <NA> <NA> 0 0 0 0
## 3 timepoints(h) <NA> <NA> 0 0 0 0
## 6 hyocholic acid inx0005 407.2801 3.2258500 <NA> <NA> <NA> <NA>
## 7 isoliquiritigenin HMDB30808 255.0682 1.4637000 <NA> <NA> <NA> <NA>
## 8 stearidonic acid HMDB06547 275.2011 4.0438833 <NA> <NA> <NA> <NA>
## 9 2-aminobutyric acid HMDB00452 104.0545 0.7084167 <NA> <NA> <NA> <NA>
## 10 urea HMDB00294 100.0000 7.1697798 <NA> <NA> <NA> <NA>
## X0.5 X0.6 X0.7 X0.8 X0.9 X0.10 X1.1 X1.2 X1.3
## 1 1 2 2 2 2 2 1 1 1
## 2 0 0 0 0 0 0 1 1 1
## 3 0 0 0 0 0 0 0.083 0.083 0.083
## 6 <NA> <NA> <NA> <NA> <NA> <NA> 2.784204e+02 2.784204e+02 2.784204e+02
## 7 <NA> <NA> <NA> <NA> <NA> <NA> 1.370141e+03 3.178774e+03 5.442983e+02
## 8 <NA> <NA> <NA> <NA> <NA> <NA> 2.247636e+01 2.247636e+01 2.247636e+01
## 9 <NA> <NA> <NA> <NA> <NA> <NA> 2.168240e+03 2.676821e+03 2.284670e+03
## 10 <NA> <NA> <NA> <NA> <NA> <NA> 3.273674e+06 4.605178e+06 2.243755e+06
## X1.4 X1.5 X1.6 X1.7 X1.8
## 1 1 1 2 2 2
## 2 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083
## 6 2.784204e+02 2.784204e+02 2.784204e+02 2.784204e+02 2.784204e+02
## 7 1.379580e+03 3.237247e+03 7.937158e+02 1.550471e+03 1.550471e+03
## 8 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01
## 9 2.709623e+03 2.245499e+03 2.249226e+03 2.030242e+03 1.910813e+03
## 10 3.408362e+06 2.834098e+06 3.589067e+06 3.199218e+06 1.909982e+06
## X1.9 X1.10 X2.1 X2.2 X2.3
## 1 2 2 1 1 1
## 2 1 1 2 2 2
## 3 0.083 0.083 0.25 0.25 0.25
## 6 2.784204e+02 2.784204e+02 3.578969e+02 3.489997e+02 3.205295e+02
## 7 1.012269e+03 8.877423e+02 3.552790e+03 4.362738e+03 6.527250e+03
## 8 2.247636e+01 2.247636e+01 5.389544e+01 5.389544e+01 5.389544e+01
## 9 1.975678e+03 2.125965e+03 1.021374e+03 2.540928e+03 2.596432e+03
## 10 3.855880e+06 3.213246e+06 3.848528e+06 5.265081e+06 1.587340e+06
## X2.4 X2.5 X2.6 X2.7 X2.8
## 1 1 1 2 2 2
## 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25
## 6 3.205295e+02 3.205295e+02 3.205295e+02 6.983260e+02 3.205295e+02
## 7 4.939517e+03 1.201432e+04 4.768880e+03 3.791118e+03 5.047187e+03
## 8 5.389544e+01 5.389544e+01 5.389544e+01 5.389544e+01 5.389544e+01
## 9 2.709623e+03 2.118093e+03 2.120029e+03 2.357740e+03 1.424533e+03
## 10 1.818286e+06 1.717971e+06 1.174493e+06 6.135470e+05 2.533136e+06
## X2.9 X2.10 X3.1 X3.2 X3.3
## 1 2 2 1 1 1
## 2 2 2 3 3 3
## 3 0.25 0.25 0.5 0.5 0.5
## 6 7.100481e+01 1.264203e+02 1.887861e+02 1.887861e+02 1.887861e+02
## 7 4.446028e+03 3.474077e+03 1.462294e+04 8.090344e+03 1.015265e+04
## 8 5.389544e+01 5.389544e+01 2.247636e+01 2.247636e+01 2.247636e+01
## 9 1.229884e+03 2.709623e+03 1.745642e+03 1.856963e+03 2.215781e+03
## 10 2.784068e+06 2.976258e+06 6.534630e+05 7.868380e+05 1.086657e+06
## X3.4 X3.5 X3.6 X3.7 X3.8
## 1 1 1 2 2 2
## 2 3 3 3 3 3
## 3 0.5 0.5 0.5 0.5 0.5
## 6 1.887861e+02 1.887861e+02 1.887861e+02 1.887861e+02 1.887861e+02
## 7 9.253099e+03 1.570578e+04 1.205226e+04 5.949388e+03 9.335844e+03
## 8 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01 2.247636e+01
## 9 2.149064e+03 1.194508e+03 1.282945e+03 1.798378e+03 1.438931e+03
## 10 7.938860e+05 9.037070e+05 9.934000e+05 3.508810e+05 3.289187e+06
## X3.9 X3.10 X4.1 X4.2 X4.3
## 1 2 2 1 1 1
## 2 3 3 4 4 4
## 3 0.5 0.5 1 1 1
## 6 1.887861e+02 1.887861e+02 385.0864 385.4431 385.4431
## 7 9.693643e+03 9.866803e+03 8864.8366 9168.3392 7920.8095
## 8 2.247636e+01 2.247636e+01 101.9314 101.9314 101.9314
## 9 1.746348e+03 1.342716e+03 1323.4021 2193.0985 2430.9826
## 10 2.692636e+06 2.394859e+06 882732.0000 1043082.0000 2654494.0000
## X4.4 X4.5 X4.6 X4.7 X4.8
## 1 1 1 2 2 2
## 2 4 4 4 4 4
## 3 1 1 1 1 1
## 6 385.7997 385.4431 385.4431 385.4431 385.4431
## 7 8249.3035 15848.4163 8067.7437 11979.5423 10973.7672
## 8 101.9314 101.9314 101.9314 101.9314 101.9314
## 9 1786.0457 1955.4832 1874.8139 1262.5695 1677.9472
## 10 1059533.0000 934680.0000 1054942.0000 1103732.0000 960388.0000
## X4.9 X4.10 X5.1 X5.2 X5.3
## 1 2 2 1 1 1
## 2 4 4 5 5 5
## 3 1 1 2 2 2
## 6 3.854431e+02 385.4431 374.5935 235.0687 235.0687
## 7 1.067116e+04 7477.9595 10010.1282 6500.5575 5321.4688
## 8 6.857615e+01 135.2867 195.2622 195.2622 195.2622
## 9 1.570819e+03 2083.4629 1345.7202 1429.7082 1308.6155
## 10 1.199171e+06 961386.0000 815521.0000 1125906.0000 956859.0000
## X5.4 X5.5 X5.6 X5.7 X5.8
## 1 1 1 2 2 2
## 2 5 5 5 5 5
## 3 2 2 2 2 2
## 6 235.0687 235.0687 247.1879 310.4244 8.068912e+00
## 7 2282.2136 8061.4780 14492.2275 6312.9234 4.548317e+03
## 8 195.2622 195.2622 195.2622 195.2622 1.952622e+02
## 9 1066.4951 1524.2739 1540.6572 1232.6300 1.528981e+03
## 10 1112064.0000 1203212.0000 865023.0000 526880.0000 3.990593e+06
## X5.9 X5.10 X6.1 X6.2 X6.3
## 1 2 2 1 1 1
## 2 5 5 6 6 6
## 3 2 2 4 4 4
## 6 235.0687 235.0687 6.069089e+02 5.469151e+02 5.469151e+02
## 7 4692.2979 8462.2400 1.588454e+04 1.006271e+04 1.449134e+04
## 8 195.2622 195.2622 7.898322e+01 7.898322e+01 7.898322e+01
## 9 1280.4679 1140.9415 1.373997e+03 9.228641e+02 1.316421e+03
## 10 1576344.0000 4330585.0000 2.218247e+06 3.507028e+06 2.218247e+06
## X6.4 X6.5 X6.6 X6.7 X6.8
## 1 1 1 2 2 2
## 2 6 6 6 6 6
## 3 4 4 4 4 4
## 6 5.469151e+02 4.869212e+02 5.469151e+02 546.91506 5.469151e+02
## 7 1.405494e+04 1.588454e+04 1.470281e+04 15884.54430 1.466780e+03
## 8 7.898322e+01 7.898322e+01 7.898322e+01 78.98322 7.898322e+01
## 9 1.632163e+03 1.593497e+03 1.501294e+03 1596.39534 1.567877e+03
## 10 3.895619e+06 1.107165e+06 3.769888e+06 842867.00000 1.059359e+06
## X6.9 X6.10 X7.1 X7.2 X7.3
## 1 2 2 1 1 1
## 2 6 6 7 7 7
## 3 4 4 6 6 6
## 6 5.469151e+02 5.469151e+02 460.8919 276.9826 276.9826
## 7 1.357760e+04 1.382118e+04 4765.3690 3683.2625 919.3350
## 8 7.898322e+01 7.898322e+01 178.2817 178.2817 178.2817
## 9 1.069840e+03 1.086028e+03 1781.4827 795.7628 1522.7288
## 10 1.247097e+06 2.316951e+06 741986.0000 1241804.0000 1708205.0000
## X7.4 X7.5 X7.6 X7.7 X7.8
## 1 1 1 2 2 2
## 2 7 7 7 7 7
## 3 6 6 6 6 6
## 6 276.9826 276.9826 276.9826 276.9826 9.307326e+01
## 7 4562.3927 7174.1774 4195.7559 5681.9093 1.083377e+04
## 8 178.2817 178.2817 178.2817 178.2817 1.782817e+02
## 9 1810.1939 1597.6780 1671.7275 1020.1537 1.419703e+03
## 10 755829.0000 544230.0000 759269.0000 559666.0000 6.651350e+05
## X7.9 X7.10 X8.1 X8.2 X8.3
## 1 2 2 1 1 1
## 2 7 7 8 8 8
## 3 6 6 8 8 8
## 6 276.9826 276.9826 1052.3366 208.9474 744.4353
## 7 11442.2029 3941.0242 499.3623 1073.4931 493.2948
## 8 178.2817 178.2817 165.2253 165.2253 165.2253
## 9 1085.0780 2142.9126 2709.6230 1646.5112 2259.9431
## 10 1111327.0000 2411841.0000 2927240.0000 2979346.0000 2780058.0000
## X8.4 X8.5 X8.6 X8.7 X8.8
## 1 1 1 2 2 2
## 2 8 8 8 8 8
## 3 8 8 8 8 8
## 6 627.3316 627.3316 627.3316 424.2711 148.1634
## 7 2909.7819 4034.3601 1724.5350 960.8781 5755.2843
## 8 165.2253 213.4903 165.2253 165.2253 165.2253
## 9 1935.4835 1576.4472 2080.9462 2366.2413 856.8270
## 10 1171232.0000 1232374.0000 1008573.0000 1037932.0000 2235284.0000
## X8.9 X8.10 X9.1 X9.2 X9.3
## 1 2 2 1 1 1
## 2 8 8 9 9 9
## 3 8 8 12 12 12
## 6 627.3316 627.3316 936.1903 564.1867 564.1867
## 7 7132.6273 2369.1902 401.4779 331.4751 705.8152
## 8 165.2253 116.9604 196.6458 416.0562 416.0562
## 9 1366.5753 2159.2240 2504.8321 961.5433 1940.8652
## 10 3087811.0000 4278483.0000 917490.0000 1056530.0000 2189306.0000
## X9.4 X9.5 X9.6 X9.7 X9.8
## 1 1 1 2 2 2
## 2 9 9 9 9 9
## 3 12 12 12 12 12
## 6 564.1867 564.1867 564.1867 564.1867 192.1831
## 7 1247.0930 2914.2993 426.9362 928.1585 569.4678
## 8 416.0562 416.0562 416.0562 416.0562 416.0562
## 9 1764.4258 1858.6772 2220.4156 2709.6230 1411.1427
## 10 1142309.0000 1930460.0000 2915531.0000 2805776.0000 1104783.0000
## X9.9 X9.10 X10.1 X10.2 X10.3
## 1 2 2 1 1 1
## 2 9 9 10 10 10
## 3 12 12 15 15 15
## 6 564.1867 564.1867 5.299150e+00 5.299150e+00 5.299150e+00
## 7 1214.9081 629.2542 7.293924e+02 7.987547e+02 7.566690e+02
## 8 416.0562 416.0562 1.817239e+02 4.154151e+01 1.817239e+02
## 9 1341.7089 2572.7710 2.020087e+03 2.319318e+03 1.925388e+03
## 10 2281254.0000 4531902.0000 1.143838e+06 1.668506e+06 5.605365e+06
## X10.4 X10.5 X10.6 X10.7 X10.8
## 1 1 1 2 2 2
## 2 10 10 10 10 10
## 3 15 15 15 15 15
## 6 5.299150e+00 5.299150e+00 5.299150e+00 5.299150e+00 5.299150e+00
## 7 5.346891e+02 1.411588e+03 3.060022e+02 3.076908e+02 7.466542e+01
## 8 3.124496e+02 1.817239e+02 1.817239e+02 2.699712e+02 1.029333e+02
## 9 1.631404e+03 1.627196e+03 1.766400e+03 1.498653e+03 1.194853e+03
## 10 2.855181e+06 2.628458e+06 1.751421e+06 4.423157e+06 2.615589e+06
## X10.9 X10.10 X11.1 X11.2 X11.3
## 1 2 2 1 1 1
## 2 10 10 11 11 11
## 3 15 15 24 24 24
## 6 5.299150e+00 5.299150e+00 1052.3366 1052.3366 1052.3366
## 7 9.333935e+02 1.441079e+03 519.4658 138.3214 355.6367
## 8 1.817239e+02 1.817239e+02 225.2154 225.2154 225.2154
## 9 1.509416e+03 2.238796e+03 1415.0529 1802.2512 1861.9488
## 10 2.497827e+06 3.362469e+06 5567127.0000 4807600.0000 5570475.0000
## X11.4 X11.5 X11.6 X11.7 X11.8
## 1 1 1 2 2 2
## 2 11 11 11 11 11
## 3 24 24 24 24 24
## 6 1052.3366 1052.3366 864.8001 1052.3366 274.7085
## 7 233.6321 757.2115 519.4658 241.7457 519.4658
## 8 225.2154 225.2154 225.2154 187.2952 225.2154
## 9 1607.0761 1704.0346 1886.1417 1542.3639 978.0477
## 10 4761617.0000 2110272.0000 1091591.0000 1780644.0000 2183886.0000
## X11.9 X11.10 X12.1 X12.2 X12.3
## 1 2 2 1 1 1
## 2 11 11 12 12 12
## 3 24 24 30 30 30
## 6 1052.3366 1052.3366 1.022622e+03 889.8966 252.2344
## 7 1156.3891 753.3245 5.750406e+01 1507.9037 623.6827
## 8 303.7545 184.5964 2.985803e+02 162.7357 416.0562
## 9 885.6081 1274.9299 1.871969e+03 1169.5236 1073.9279
## 10 4742487.0000 1058786.0000 2.859222e+06 3956591.0000 4524865.0000
## X12.4 X12.5 X12.6 X12.7 X12.8
## 1 1 1 2 2 2
## 2 12 12 12 12 12
## 3 30 30 30 30 30
## 6 889.8966 889.8966 889.8966 889.8966 1052.3366
## 7 220.3680 1193.5548 658.5670 623.6827 623.6827
## 8 298.5803 298.5803 298.5803 225.1035 298.5803
## 9 1664.1779 1249.8718 1433.8242 1066.0946 1140.9290
## 10 336349.0000 2022739.0000 3297338.0000 2506869.0000 3931178.0000
## X12.9 X12.10 X13.1 X13.2 X13.3
## 1 2 2 1 1 1
## 2 12 12 13 13 13
## 3 30 30 36 36 36
## 6 889.8966 889.8966 429.2066 830.2536 881.8535
## 7 124.4961 603.3856 935.0894 501.2326 935.0894
## 8 298.5803 298.5803 206.8002 416.0562 416.0562
## 9 939.2061 1368.8430 1751.6133 878.9021 1804.2838
## 10 3735142.0000 4330657.0000 3434255.0000 2616869.0000 3276844.0000
## X13.4 X13.5 X13.6 X13.7 X13.8
## 1 1 1 2 2 2
## 2 13 13 13 13 13
## 3 36 36 36 36 36
## 6 443.4000 443.4000 16.0817 483.7999 1.920454e+01
## 7 935.0894 1677.8042 119.5775 935.0894 9.350894e+02
## 8 416.0562 416.0562 416.0562 416.0562 4.160562e+02
## 9 2081.1306 1262.9347 1698.5452 1474.8592 1.494758e+03
## 10 1809303.0000 2134561.0000 2141069.0000 707808.0000 1.952686e+06
## X13.9 X13.10 X14.1 X14.2 X14.3
## 1 2 2 1 1 1
## 2 13 13 14 14 14
## 3 36 36 48 48 48
## 6 443.4000 443.4000 1052.3366 715.0406 576.2052
## 7 935.0894 1441.7434 1054.2212 1160.2287 224.5996
## 8 416.0562 416.0562 214.8719 214.8719 214.8719
## 9 869.5958 1934.3173 1436.0103 1649.2100 1854.4869
## 10 665453.0000 2248179.0000 1783857.0000 2928799.0000 2932614.0000
## X14.4 X14.5 X14.6 X14.7 X14.8
## 1 1 1 2 2 2
## 2 14 14 14 14 14
## 3 48 48 48 48 48
## 6 576.2052 576.2052 576.2052 287.8035 9.674108e+01
## 7 1054.2212 3518.8923 422.0578 1054.2212 1.054221e+03
## 8 214.8719 214.8719 214.8719 214.8719 2.148719e+02
## 9 1138.8949 1449.6058 1220.1843 1452.1421 9.352852e+02
## 10 768613.0000 1146017.0000 3502838.0000 1770733.0000 1.516211e+06
## X14.9 X14.10
## 1 2 2
## 2 14 14
## 3 48 48
## 6 576.2052 576.2052
## 7 416.2823 583.2665
## 8 214.8719 214.8719
## 9 908.0581 1193.4161
## 10 998402.0000 2259062.0000PKsA function to calculate the 7 pharmacokinetics parameters (Tmax, Cmax, AUC, CL, Tlast, Tfirst, Cmin) and plot the time-intensity curves for specified compounds.
A list of metabolites and 7 pharmacokinetics parameters (Tmax,Cmax,AUC,CL,Tlast,Tfirst,Cmin) of specified compound:
data("B")
data("design")
pks<-PKs(B,d.point="mean",d.ebar="SE",filepath=getwd(),design=design)
knitr::kable(pks[c(1:10),],align = 'c')| Name | ID | m.z | R.T.min. | Tmax | Tlast | Tfirst | Cmax | Cmin | AUC | CL | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 14 | octanoyl-rac-glycerol | inx0001 | 219.1401 | 3.5638000 | 0 | 14 | 0 | 4126.793 | 2411.566 | 42776.5376 | 0.0024546 |
| 12 | hippuric acid | HMDB00714 | 178.0503 | 0.7566000 | 0 | 0 | 0 | 5854.191 | 0.000 | 2927.0957 | 0.0358717 |
| 13 | hexadecanedioic acid | HMDB00672 | 285.2062 | 4.0334167 | 0 | 0 | 0 | 1788.707 | 0.000 | 894.3536 | 0.1174032 |
| 21 | n-dodecanoic acid | HMDB00638 | 199.1693 | 5.2730000 | 6 | 14 | 0 | 111657.052 | 24738.157 | 795079.4137 | 0.0001321 |
| 31 | 3-hydroxybutyric acid | HMDB00357 | 103.0400 | 0.6600000 | 6 | 14 | 0 | 19741.845 | 6230.879 | 156005.0770 | 0.0006731 |
| 4 | taurine | HMDB00251 | 124.0100 | 0.6800000 | 0 | 14 | 0 | 55897.293 | 40702.789 | 693164.0723 | 0.0001515 |
| 5 | phenylpyruvic acid | HMDB00205 | 165.0545 | 3.5218833 | 13 | 14 | 0 | 19578.073 | 12113.349 | 217150.4032 | 0.0004835 |
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
The time-intensity curves for specified compounds are in the folder named “PKs” which is created automatically.
CorrPlotA function to calculate the correlation coefficients and plot the correlation diagram (8 types) of two input datasets.
data("B")
data("C")
CorrPlot(dataset1=B,dataset2=C,cor.method="pearson",filepath=getwd(),fig.form="heatmap",design = design)ScatPlotA function to plot the PCA or PLSDA score figures and trajectories on input data:
data("A")
ScatPlot(scat.data=A,scform="PCA",num.of.cp=2,filepath=getwd(),design)HeatMapA function to plot the heatmap and clusters of input data:
data("A")
HeatMap(data=A,cluster="both",scale="row",filepath=getwd(),design)help(package = 'polyPK', help_type = 'html')
# or see a standalone list of vignettes
browseVignettes('polyPK')