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Summarization

Source: vignettes/summarization.qmd

Preliminary 

## load R package
library(msDiaLogue)
## preprocessing
fileName <- "../inst/extdata/Toy_Spectronaut_Data.csv"
dataSet <- preprocessing(fileName,
                         filterNaN = TRUE, filterUnique = 2,
                         replaceBlank = TRUE, saveRm = TRUE)
## transformation
dataTran <- transform(dataSet, logFold = 2)
## annotation-based filtering
dataFiltAnno <- filterOutIn(dataTran, listName = "ALBU_BOVIN",
                            removeList = TRUE, saveRm = TRUE)
## normalization
dataNorm <- normalize(dataFiltAnno, normalizeType = "median")
## data-driven filtering
dataFilt <- filterNA(dataNorm, minProp = 0.51, by = "cond", saveRm = TRUE)
## imputation
dataImput <- impute.min_local(dataFilt)

Example 

dataSumm <- summarize(dataImput, saveSumm = TRUE)
R.Condition Stat NUD4B_HUMAN (+1) A0A7P0T808_HUMAN (+1) A0A8I5KU53_HUMAN (+1) ZN840_HUMAN CC85C_HUMAN C9JEV0_HUMAN (+1) C9JNU9_HUMAN CYC_BOVIN TRFE_BOVIN F8W0H2_HUMAN H0Y7V7_HUMAN (+1) H0YD14_HUMAN H3BUF6_HUMAN H7C1W4_HUMAN (+1) H7C3M7_HUMAN TLR3_HUMAN LRIG2_HUMAN RAB3D_HUMAN ADH1_YEAST LYSC_CHICK BGAL_ECOLI CYTA_HUMAN KPCB_HUMAN LIPL_HUMAN CO6_HUMAN BGAL_HUMAN SYTC_HUMAN CASPE_HUMAN DCAF6_HUMAN DALD3_HUMAN HGNAT_HUMAN RFFL_HUMAN RN185_HUMAN ZN462_HUMAN ALKB7_HUMAN POLK_HUMAN ACAD8_HUMAN
100fmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
100fmol mean 0.8970585 2.1918625 1.1190602 -1.3091319 -0.7616711 -2.5823326 -1.3720362 3.5549310 4.1598999 -0.4095082 0.5375144 0.4206618 -1.5899192 -1.7349727 0.3759821 -1.9399514 -0.9633006 0.5924669 5.0671570 3.9307808 4.8065148 -0.6487769 0.4907685 -1.2108609 -2.6386252 2.1157812 4.8885237 -3.0010370 -1.6555058 0.1042002 0.8543029 -2.6865201 0.4758179 -0.8105107 -2.4501697 -1.7550160 -1.8485990
100fmol sd 0.3769622 0.3785925 0.6660458 0.5726491 0.3310524 0.7067318 0.5040580 0.3785632 0.2291963 0.3644939 0.3342775 0.3512733 0.1949385 0.3414639 0.2965182 0.4477853 0.5914222 0.1882251 0.1547473 0.2664000 0.3133505 0.3046148 0.4299739 0.4439982 0.3528549 0.1769605 0.2880003 0.5241712 0.4586023 0.6149859 0.3984081 0.4735034 0.3519661 0.6126179 0.2488006 1.1738015 0.3409110
100fmol median 0.8903155 2.2254556 1.1798190 -1.2778858 -0.7063386 -2.6505697 -1.1835077 3.5900301 4.1266841 -0.4297177 0.6362034 0.4193368 -1.6406099 -1.7281049 0.4413473 -1.9038165 -0.8489855 0.5838246 5.0009454 3.9721165 4.6654466 -0.7028811 0.5220523 -1.1482665 -2.5593105 2.1457701 4.8204119 -3.2263747 -1.6768055 0.2968265 1.0374321 -2.6589903 0.4464988 -1.0154069 -2.4414801 -2.2754608 -1.8533986
100fmol trimmed 0.8970585 2.1918625 1.1190602 -1.3091319 -0.7616711 -2.5823326 -1.3720362 3.5549310 4.1598999 -0.4095082 0.5375144 0.4206618 -1.5899192 -1.7349727 0.3759821 -1.9399514 -0.9633006 0.5924669 5.0671570 3.9307808 4.8065148 -0.6487769 0.4907685 -1.2108609 -2.6386252 2.1157812 4.8885237 -3.0010370 -1.6555058 0.1042002 0.8543029 -2.6865201 0.4758179 -0.8105107 -2.4501697 -1.7550160 -1.8485990
100fmol mad 0.4381887 0.3061554 0.5539722 0.5922179 0.3050541 0.7804154 0.1568787 0.4039147 0.2003591 0.4067100 0.2079114 0.3900043 0.1514542 0.3965858 0.2544084 0.5144065 0.4396392 0.1998783 0.0382715 0.2288437 0.0485122 0.2302859 0.4821110 0.3388407 0.2304363 0.1261657 0.2234758 0.1414845 0.4122098 0.3366253 0.0618589 0.5586161 0.3829990 0.2734671 0.2427813 0.1648448 0.3479888
100fmol min 0.4784339 1.6974365 0.2493124 -2.0149419 -1.1828195 -3.2366723 -2.1163940 3.1042574 3.9250040 -0.7955644 0.0695863 0.0071198 -1.7427644 -2.1263242 -0.0006345 -2.4072922 -1.7721382 0.3807319 4.9698771 3.5787606 4.6203712 -0.9551142 0.0000000 -1.8078448 -3.1315263 1.8740517 4.6394239 -3.3253722 -2.1936992 -0.7734746 0.2593672 -3.1810405 0.1210060 -1.2914442 -2.7601984 -2.4691425 -2.2558682
100fmol max 1.3291690 2.6191023 1.8672903 -0.6658141 -0.4511877 -1.7915185 -1.0047353 3.9354062 4.4612272 0.0169672 0.8080643 0.8368538 -1.3356925 -1.3573568 0.6218682 -1.5448805 -0.3830931 0.8214865 5.2968601 4.2001297 5.2747947 -0.2342312 0.9189694 -0.7390658 -2.3043532 2.2975330 5.2738470 -2.2260264 -1.0747131 0.5966224 1.0829802 -2.2470594 0.8892680 0.0802151 -2.1575204 0.0000000 -1.4317308
100fmol range 0.8507350 0.9216658 1.6179778 1.3491277 0.7316318 1.4451538 1.1116587 0.8311487 0.5362232 0.8125316 0.7384780 0.8297340 0.4070719 0.7689674 0.6225027 0.8624118 1.3890450 0.4407547 0.3269830 0.6213690 0.6544235 0.7208830 0.9189694 1.0687790 0.8271731 0.4234812 0.6344231 1.0993457 1.1189860 1.3700971 0.8236130 0.9339811 0.7682620 1.3716592 0.6026780 2.4691425 0.8241373
100fmol skew 0.0280993 -0.1968546 -0.2007667 -0.1048600 -0.2502010 0.0882493 -0.6798135 -0.1289755 0.2779958 0.0824052 -0.4935760 0.0072972 0.3181030 -0.0312702 -0.2648206 -0.0445041 -0.3864236 0.0858037 0.7050559 -0.2952034 0.7335017 0.3632269 -0.0867136 -0.3038766 -0.4547603 -0.3611834 0.3682825 0.6893058 0.1031837 -0.5534023 -0.7303937 -0.0394298 0.1119722 0.6172372 -0.0752463 0.7353255 0.0300390
100fmol kurtosis -2.1623555 -1.8672470 -1.8746284 -2.0182453 -2.1078309 -2.3170589 -1.7290371 -2.1969982 -1.9674099 -2.1828813 -1.8958471 -2.0216077 -2.0866584 -2.1677045 -2.1408107 -2.3843393 -1.8869101 -2.0431604 -1.7206403 -1.9654126 -1.6988259 -1.8821598 -2.2639059 -1.8632250 -1.8413464 -1.8499292 -2.0127789 -1.7340247 -1.8826362 -1.8348311 -1.7016651 -2.3763015 -2.2161147 -1.7735440 -1.9181152 -1.6967190 -1.9310689
100fmol se 0.1884811 0.1892963 0.3330229 0.2863245 0.1655262 0.3533659 0.2520290 0.1892816 0.1145982 0.1822470 0.1671387 0.1756367 0.0974692 0.1707320 0.1482591 0.2238926 0.2957111 0.0941125 0.0773737 0.1332000 0.1566752 0.1523074 0.2149869 0.2219991 0.1764275 0.0884802 0.1440001 0.2620856 0.2293011 0.3074929 0.1992040 0.2367517 0.1759831 0.3063089 0.1244003 0.5869007 0.1704555
200fmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
200fmol mean 1.2129798 0.9476617 1.6646748 -0.8707864 -0.9704449 -2.4355408 -1.0109247 4.8036461 4.9771724 -0.1293629 0.8123346 0.9012464 -1.0788546 -1.6920949 0.8326191 -1.8320831 -0.7943162 0.7906959 6.3018992 5.1797871 6.1037095 -0.3601495 0.8966850 -0.7324823 -2.4259129 2.4717449 5.4536305 -3.2541540 -1.7246925 0.7037732 1.1711891 -2.3300528 -0.0848047 -0.4918852 -1.5365371 -2.0645198 -1.4177061
200fmol sd 0.1071089 1.9488538 0.2978067 0.2511455 0.8124918 0.1722723 0.5178715 0.2459422 0.2402410 0.1418964 0.2875434 0.2704811 0.2334108 0.6025484 0.2781186 0.2841009 0.3659097 0.2156313 0.3588447 0.2308110 0.1072559 0.3392751 0.3037604 0.1651338 0.1373789 0.2724017 0.2251841 0.2639713 0.5003941 0.1168058 0.8173356 0.2534345 0.5072005 0.2982636 0.5252306 0.2455688 1.0630076
200fmol median 1.2134803 0.8959757 1.5330792 -0.9620397 -0.7679555 -2.4034921 -1.0787553 4.7536081 4.9015025 -0.1068813 0.7605641 0.8245895 -1.1651955 -1.5763398 0.7904305 -1.9111445 -0.9197400 0.7227233 6.1700033 5.2494074 6.0772704 -0.3758269 0.9029418 -0.7639423 -2.3620279 2.4052571 5.3639509 -3.3525387 -1.5776476 0.6520665 1.5294733 -2.3598634 0.0801284 -0.4289191 -1.4190128 -2.1309675 -1.3317100
200fmol trimmed 1.2129798 0.9476617 1.6646748 -0.8707864 -0.9704449 -2.4355408 -1.0109247 4.8036461 4.9771724 -0.1293629 0.8123346 0.9012464 -1.0788546 -1.6920949 0.8326191 -1.8320831 -0.7943162 0.7906959 6.3018992 5.1797871 6.1037095 -0.3601495 0.8966850 -0.7324823 -2.4259129 2.4717449 5.4536305 -3.2541540 -1.7246925 0.7037732 1.1711891 -2.3300528 -0.0848047 -0.4918852 -1.5365371 -2.0645198 -1.4177061
200fmol mad 0.1126297 2.4219831 0.0452251 0.1242739 0.4914004 0.1611430 0.5489776 0.2236113 0.1149913 0.1021678 0.2457022 0.1942066 0.1038801 0.5038550 0.2800156 0.1858911 0.2033674 0.1295565 0.1052464 0.1448284 0.0542932 0.4092192 0.3556479 0.1459374 0.0185186 0.1390690 0.0519450 0.1049969 0.2660872 0.0223739 0.1125132 0.2746955 0.2037319 0.2486957 0.2867982 0.1401598 1.2080754
200fmol min 1.0835077 -0.7610814 1.4827675 -1.0458613 -2.1179882 -2.6460631 -1.4490356 4.6026580 4.7809474 -0.3222491 0.5369436 0.6935989 -1.2434857 -2.4900058 0.5904082 -2.0692114 -1.0569094 0.6251033 6.0359272 4.8584982 6.0042215 -0.6677980 0.5516635 -0.8818061 -2.6312903 2.2181351 5.2984508 -3.4430880 -2.4423034 0.6330298 -0.0504002 -2.5472597 -0.8247065 -0.8831795 -2.2754926 -2.2811087 -2.5736366
200fmol max 1.3414509 2.7597767 2.1097733 -0.5132050 -0.2278802 -2.2891161 -0.4371524 5.1047101 5.3247374 0.0185604 1.1912667 1.2622077 -0.7415416 -1.1256944 1.1592071 -1.4368320 -0.2808755 1.0922337 6.8316629 5.3618355 6.2560758 -0.0211462 1.2291929 -0.5202384 -2.3483056 2.8583306 5.7881694 -2.8684507 -1.3011714 0.8779300 1.6762101 -2.0532247 0.3252309 -0.2265231 -1.0326304 -1.7150353 -0.4337676
200fmol range 0.2579432 3.5208581 0.6270057 0.5326563 1.8901080 0.3569470 1.0118832 0.5020521 0.5437900 0.3408095 0.6543231 0.5686087 0.5019441 1.3643114 0.5687989 0.6323794 0.7760339 0.4671304 0.7957357 0.5033373 0.2518543 0.6466518 0.6775294 0.3615677 0.2829847 0.6401955 0.4897186 0.5746373 1.1411320 0.2449002 1.7266103 0.4940349 1.1499374 0.6566564 1.2428621 0.5660734 2.1398690
200fmol skew -0.0098116 0.0053054 0.7336795 0.5521995 -0.4972246 -0.1997451 0.0870806 0.2033498 0.5953872 -0.3409315 0.3116366 0.3699725 0.6025479 -0.3276981 0.1450278 0.4726115 0.5059092 0.4942334 0.6775000 -0.4794904 0.5096975 0.0222253 -0.0305369 0.2770931 -0.7352542 0.5055549 0.7060789 0.6413912 -0.5611088 0.7236852 -0.7335529 0.0754583 -0.6251522 -0.3206690 -0.4698451 0.5289832 -0.0654357
200fmol kurtosis -1.9475500 -2.4309454 -1.6979189 -1.8545257 -1.8243200 -2.2103727 -2.3380977 -2.2091757 -1.7822298 -1.8502167 -2.0115691 -2.0329920 -1.8070789 -2.0089282 -2.2690241 -1.9086937 -1.8981975 -1.9057581 -1.7277030 -1.9168882 -1.7949344 -2.4054081 -2.1920172 -2.0988331 -1.6980420 -1.7962891 -1.7130477 -1.7688991 -1.8031565 -1.7062670 -1.6975802 -2.3510319 -1.7543440 -2.0553793 -1.8074203 -1.8146451 -2.3453427
200fmol se 0.0535545 0.9744269 0.1489034 0.1255727 0.4062459 0.0861362 0.2589358 0.1229711 0.1201205 0.0709482 0.1437717 0.1352406 0.1167054 0.3012742 0.1390593 0.1420505 0.1829549 0.1078156 0.1794223 0.1154055 0.0536279 0.1696375 0.1518802 0.0825669 0.0686894 0.1362009 0.1125921 0.1319856 0.2501970 0.0584029 0.4086678 0.1267173 0.2536003 0.1491318 0.2626153 0.1227844 0.5315038
50fmol n 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000 4.0000000
50fmol mean 1.5018335 -1.4867645 0.7414668 -1.2046036 -0.6978038 -0.7687851 -0.7991065 3.7761356 4.5984741 0.1523311 0.2432124 1.2303125 -0.7489724 -2.6300921 0.6353621 -1.8284465 -0.9168044 1.2127423 5.0713696 3.7915558 4.9848046 1.2366567 1.1905031 -0.7024215 -1.8418109 3.0118366 5.6824480 -0.7531886 -1.7462293 -0.4885937 0.7407263 -2.7704565 0.0157819 -1.0501134 -1.3023443 -2.7093144 -2.2373695
50fmol sd 0.3542605 2.1345395 1.6486492 0.7383043 0.3072258 0.8341488 0.5336857 0.1628911 0.2824951 0.2217272 0.2765579 0.1969418 0.2199691 1.1691397 0.4126341 0.0802473 0.3171125 0.1671128 0.1845805 0.1619713 0.2297245 0.7884112 0.1878945 0.4334406 0.2595509 0.2260399 0.2848702 0.7745592 0.3718414 0.3383616 0.7296510 0.9025735 0.4445735 1.7332029 0.6331575 1.3398892 0.3129499
50fmol median 1.4844426 -1.6536766 1.3507094 -1.1007560 -0.6179448 -0.8132309 -0.5510695 3.7839857 4.5543837 0.0830871 0.1394245 1.2236870 -0.6996272 -2.2779955 0.7811797 -1.8388219 -0.9912944 1.2243984 5.0195531 3.8194856 4.9308360 1.0430731 1.1350207 -0.7135207 -1.9710344 3.0270652 5.7316265 -1.0985272 -1.7436689 -0.6190757 0.9824788 -2.4390129 0.0927265 -0.2804544 -1.5134598 -2.2365479 -2.1960684
50fmol trimmed 1.5018335 -1.4867645 0.7414668 -1.2046036 -0.6978038 -0.7687851 -0.7991065 3.7761356 4.5984741 0.1523311 0.2432124 1.2303125 -0.7489724 -2.6300921 0.6353621 -1.8284465 -0.9168044 1.2127423 5.0713696 3.7915558 4.9848046 1.2366567 1.1905031 -0.7024215 -1.8418109 3.0118366 5.6824480 -0.7531886 -1.7462293 -0.4885937 0.7407263 -2.7704565 0.0157819 -1.0501134 -1.3023443 -2.7093144 -2.2373695
50fmol mad 0.3672731 2.4707832 0.5965965 0.6422796 0.2264772 0.7999470 0.0662954 0.1557152 0.2724059 0.1422271 0.1267210 0.1777350 0.1495158 0.6850005 0.2119126 0.0853299 0.2655771 0.1937251 0.0950713 0.1544785 0.1762235 0.6283288 0.1290924 0.5395819 0.0024444 0.2655935 0.2173364 0.0966336 0.3849543 0.1440314 0.3198562 0.4195510 0.3824926 0.2807877 0.2599376 0.5817346 0.3100489
50fmol min 1.1006904 -3.3201971 -1.6818749 -2.1765737 -1.1117833 -1.7312115 -1.5975565 3.5711635 4.3372528 -0.0128438 0.0539524 0.9962309 -1.0547978 -4.2845713 0.0489373 -1.8963761 -1.1704237 1.0352351 4.9101618 3.5935653 4.7834979 0.5947847 1.0479490 -1.0774637 -1.9726831 2.7846510 5.2956584 -1.2210747 -2.1979198 -0.7162235 -0.3212160 -4.0679005 -0.5696866 -3.6395447 -1.8044113 -4.6591861 -2.6241451
50fmol max 1.9377582 0.6804921 1.9463231 -0.4403285 -0.4435426 0.2825328 -0.4967305 3.9654072 4.9478763 0.4559941 0.6400481 1.4776452 -0.5418374 -1.6798060 0.9301517 -1.7397662 -0.5142051 1.3669372 5.3362105 3.9336869 5.2940486 2.2656960 1.4440220 -0.3051809 -1.4524915 3.2085651 5.9708805 0.4053746 -1.2996597 0.0000000 1.3191634 -2.1358999 0.4473614 0.0000000 -0.3780465 -1.7049755 -1.9331960
50fmol range 0.8370678 4.0006892 3.6281981 1.7362452 0.6682407 2.0137443 1.1008260 0.3942436 0.6106235 0.4688379 0.5860957 0.4814143 0.5129604 2.6047653 0.8812144 0.1566099 0.6562186 0.3317022 0.4260488 0.3401216 0.5105507 1.6709113 0.3960730 0.7722828 0.5201916 0.4239142 0.6752220 1.6264493 0.8982601 0.7162235 1.6403794 1.9320006 1.0170480 3.6395447 1.4263648 2.9542106 0.6909491
50fmol skew 0.0954595 0.0315122 -0.6622248 -0.2752800 -0.3901458 0.1134678 -0.7385152 -0.1036301 0.2071519 0.4359161 0.5782893 0.0751866 -0.4440613 -0.5254781 -0.5460375 0.0849035 0.2647824 -0.0501829 0.5564729 -0.1976723 0.3805895 0.3190907 0.3969168 0.0034043 0.7499194 -0.0270460 -0.3544326 0.7371462 -0.0146451 0.6002583 -0.6195907 -0.5842510 -0.3054812 -0.7321596 0.6301201 -0.6243156 -0.1924476
50fmol kurtosis -2.0101479 -2.4012611 -1.7455982 -1.9541288 -2.0027508 -1.9251337 -1.6955661 -1.9167897 -2.1710601 -1.9664748 -1.8304951 -1.8791379 -1.8612722 -1.8600341 -1.8599569 -2.3405542 -2.1429655 -2.3654847 -1.7893241 -2.2058206 -1.9925009 -2.0835219 -2.0055726 -2.4335708 -1.6875540 -2.4060592 -1.8832973 -1.6954813 -1.9347361 -1.8106171 -1.7678150 -1.8244298 -2.0050795 -1.6994125 -1.7565948 -1.7781443 -2.1501921
50fmol se 0.1771302 1.0672697 0.8243246 0.3691521 0.1536129 0.4170744 0.2668429 0.0814455 0.1412475 0.1108636 0.1382789 0.0984709 0.1099845 0.5845699 0.2063170 0.0401237 0.1585563 0.0835564 0.0922902 0.0809856 0.1148623 0.3942056 0.0939472 0.2167203 0.1297754 0.1130200 0.1424351 0.3872796 0.1859207 0.1691808 0.3648255 0.4512867 0.2222867 0.8666015 0.3165787 0.6699446 0.1564750

Details

The summarization() provides a table of values for each protein in the final dataset that include the final processed abundances and fold changes in each condition, and that protein’s statistical relation to the global dataset in terms of its mean, median, standard deviation, and other parameters.

The column "Stat" in the generated result includes the following statistics:

  • n: Number.
  • mean: Mean.
  • sd: Standard deviation.
  • median: Median.
  • trimmed: Trimmed mean with a trim of 0.1.
  • mad: Median absolute deviation (from the median).
  • min: Minimum.
  • max: Maximum.
  • range: The difference between the maximum and minimum value.
  • skew: Skewness.
  • kurtosis: Kurtosis.
  • se: Standard error.

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