Skip to contents

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
100pmol 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
100pmol mean 0.8339289 2.1946993 1.1272591 -1.3591912 -0.6945202 -2.6606531 -1.3909779 3.6126755 4.1230623 -0.3960066 0.4497424 0.3836439 -1.6498392 -1.7502104 0.4292735 -2.0802871 -1.0055235 0.4644049 4.9387246 3.9802151 4.7294637 -0.6587380 0.3263654 -1.2593633 -2.7175518 1.9940356 4.9127697 -3.0160906 -1.7121101 0.0492920 0.8838116 -2.6163500 0.4274039 -0.7985565 -2.6047652 -1.8281529 -1.9723364
100pmol sd 0.2348700 0.3979606 0.4406670 0.3717256 0.2268024 0.6601444 0.5065498 0.1557715 0.1936523 0.2687450 0.0918448 0.2942137 0.1814039 0.1591378 0.4384205 0.2842717 0.3225505 0.1409587 0.1644398 0.1645973 0.1811004 0.3314665 0.2183662 0.1960120 0.1464642 0.1347818 0.1661390 0.5011964 0.5114720 0.6348369 0.1958017 0.3997397 0.3248747 0.5418324 0.1245565 1.2271137 0.2641545
100pmol median 0.7579987 2.2403157 1.2432466 -1.4251512 -0.6803538 -2.6004194 -1.3440587 3.5861517 4.0751142 -0.4605735 0.4402971 0.3297070 -1.6635252 -1.7138370 0.3465380 -2.0258424 -1.0175209 0.4333598 4.8807061 3.9495962 4.6597723 -0.6822958 0.3856189 -1.2577681 -2.7063159 1.9628946 4.8608659 -3.2191716 -1.7640435 0.2859869 0.9672070 -2.5025981 0.3891829 -0.9991834 -2.6165572 -2.3389743 -2.0306795
100pmol trimmed 0.8339289 2.1946993 1.1272591 -1.3591912 -0.6945202 -2.6606531 -1.3909779 3.6126755 4.1230623 -0.3960066 0.4497424 0.3836439 -1.6498392 -1.7502104 0.4292735 -2.0802871 -1.0055235 0.4644049 4.9387246 3.9802151 4.7294637 -0.6587380 0.3263654 -1.2593633 -2.7175518 1.9940356 4.9127697 -3.0160906 -1.7121101 0.0492920 0.8838116 -2.6163500 0.4274039 -0.7985565 -2.6047652 -1.8281529 -1.9723364
100pmol mad 0.1393805 0.3860571 0.2438687 0.3448327 0.1927737 0.7237012 0.4468410 0.1008476 0.0998788 0.1876353 0.0830200 0.2177498 0.2108517 0.0869396 0.3396860 0.2442572 0.3342375 0.0990232 0.0652936 0.1016821 0.0648882 0.2696485 0.1137707 0.2339360 0.1177429 0.0813898 0.0750340 0.1406911 0.5444626 0.2454740 0.0541263 0.2580205 0.3479345 0.1817422 0.0971534 0.2476424 0.1653811
100pmol min 0.6578963 1.6912275 0.4994500 -1.6925457 -0.9854966 -3.4192914 -2.0487396 3.4521540 3.9437609 -0.6386260 0.3495332 0.0895033 -1.8057427 -1.9745653 0.0000000 -2.4518931 -1.3776219 0.3315355 4.8140727 3.8139558 4.6028211 -1.0397232 0.0138251 -1.4787373 -2.9074443 1.8666657 4.7755655 -3.3525778 -2.2127750 -0.8802224 0.5943610 -3.1730781 0.1359572 -1.1958590 -2.7445785 -2.6346630 -2.2255399
100pmol max 1.1618220 2.6069381 1.5230932 -0.8939165 -0.4318767 -2.0224822 -0.8270544 3.8262446 4.3982600 -0.0242533 0.5688423 0.7856583 -1.4665636 -1.5986022 1.0240181 -1.8175707 -0.6094305 0.6593645 5.1794134 4.2077123 4.9954890 -0.2306371 0.5203989 -1.0431798 -2.5501313 2.1836875 5.1537815 -2.2734413 -1.1075784 0.5054164 1.0064713 -2.2871257 0.7952927 0.0000000 -2.4413680 0.0000000 -1.6024466
100pmol range 0.5039257 0.9157106 1.0236432 0.7986292 0.5536199 1.3968092 1.2216852 0.3740906 0.4544991 0.6143727 0.2193091 0.6961550 0.3391792 0.3759630 1.0240181 0.6343225 0.7681914 0.3278290 0.3653407 0.3937566 0.3926680 0.8090861 0.5065739 0.4355575 0.3573129 0.3170217 0.3782160 1.0791364 1.1051967 1.3856388 0.4121103 0.8859524 0.6593356 1.1958590 0.3032106 2.6346630 0.6230933
100pmol skew 0.4901295 -0.2017863 -0.5277014 0.2317926 -0.1393194 -0.1033601 -0.1980544 0.3682173 0.5113338 0.4427358 0.2116447 0.3757882 0.0293510 -0.4783362 0.3676981 -0.3053627 0.0746963 0.4299614 0.6440869 0.3991923 0.6619661 0.1587563 -0.5446303 -0.0118288 -0.1711784 0.4758344 0.6028465 0.6967244 0.1302489 -0.6487739 -0.6885576 -0.4772152 0.1036128 0.6719236 0.2102971 0.7189975 0.4570577
100pmol kurtosis -1.9122602 -2.0544409 -1.8022470 -2.1574069 -1.8730707 -2.2702202 -1.9040484 -1.8342804 -1.7947370 -1.9003439 -1.9356221 -1.8743213 -2.4037370 -1.8050551 -1.9139052 -2.0503862 -1.9852514 -1.8779303 -1.7557522 -1.8268086 -1.7521733 -1.8680419 -1.7906797 -2.2025667 -1.8667627 -1.8174835 -1.7690714 -1.7242625 -2.2241622 -1.7613337 -1.7345214 -1.9083169 -2.3105617 -1.7354905 -1.8626775 -1.7062813 -1.8248587
100pmol se 0.1174350 0.1989803 0.2203335 0.1858628 0.1134012 0.3300722 0.2532749 0.0778858 0.0968262 0.1343725 0.0459224 0.1471068 0.0907019 0.0795689 0.2192102 0.1421359 0.1612752 0.0704793 0.0822199 0.0822987 0.0905502 0.1657332 0.1091831 0.0980060 0.0732321 0.0673909 0.0830695 0.2505982 0.2557360 0.3174185 0.0979008 0.1998698 0.1624373 0.2709162 0.0622783 0.6135568 0.1320773
200pmol 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
200pmol mean 1.2336884 0.8520174 1.7473171 -0.7435052 -0.9037446 -2.4490371 -1.0087444 4.9572657 5.0790338 -0.1855546 0.8202930 0.8679319 -1.1461040 -1.8026059 0.8089980 -1.7879986 -0.8612458 0.8920254 6.2945905 5.2772339 6.0419963 -0.4200350 0.8428142 -0.7889052 -2.2706947 2.4899442 5.3920344 -3.1962217 -1.7764857 0.6707801 1.1673947 -2.4253856 0.0346007 -0.4209149 -1.6001975 -2.0737954 -1.2863471
200pmol sd 0.2593465 1.8363946 0.2619637 0.2585153 0.8061447 0.2214264 0.5041316 0.2374881 0.2204965 0.1719643 0.2960269 0.1499830 0.3176775 0.4679668 0.3211476 0.2350586 0.2234090 0.2207466 0.2834655 0.2760985 0.2441346 0.3348944 0.1903700 0.1321569 0.2108776 0.2489882 0.2367756 0.2907393 0.3357166 0.2643781 0.8824437 0.3000626 0.5562237 0.3683197 0.6782711 0.2510574 0.8964610
200pmol median 1.2609766 0.7639703 1.7400208 -0.8370078 -0.6996904 -2.5200743 -1.0870704 4.9759656 5.0457603 -0.1869844 0.8749265 0.8277394 -1.1893331 -1.7067187 0.8300281 -1.7822272 -0.9247863 0.9023352 6.2783867 5.2625286 6.0379651 -0.4242442 0.8342432 -0.7857552 -2.2209933 2.4681324 5.3811169 -3.1722750 -1.7313763 0.7130405 1.5312488 -2.4167395 0.1674884 -0.3727801 -1.4025392 -2.1334603 -1.1405255
200pmol trimmed 1.2336884 0.8520174 1.7473171 -0.7435052 -0.9037446 -2.4490371 -1.0087444 4.9572657 5.0790338 -0.1855546 0.8202930 0.8679319 -1.1461040 -1.8026059 0.8089980 -1.7879986 -0.8612458 0.8920254 6.2945905 5.2772339 6.0419963 -0.4200350 0.8428142 -0.7889052 -2.2706947 2.4899442 5.3920344 -3.1962217 -1.7764857 0.6707801 1.1673947 -2.4253856 0.0346007 -0.4209149 -1.6001975 -2.0737954 -1.2863471
200pmol mad 0.2105282 2.2037480 0.2876475 0.1292158 0.5084925 0.1052697 0.5099834 0.2203309 0.1656457 0.1946917 0.2354990 0.1135659 0.2612827 0.3297568 0.2698899 0.2599736 0.1598300 0.2043079 0.2561879 0.2410066 0.2384930 0.3581094 0.2048369 0.1465506 0.1625803 0.1930473 0.2173456 0.3271297 0.2752014 0.2607633 0.2605424 0.3360504 0.3107010 0.3747117 0.3013428 0.1397413 0.8775972
200pmol min 0.8920522 -0.8407850 1.4489509 -0.9241627 -2.0376118 -2.6275134 -1.4310495 4.6531117 4.8475914 -0.3843617 0.4211597 0.7511402 -1.4825147 -2.4486004 0.3960272 -2.0676338 -1.0325902 0.6131741 5.9659708 4.9548813 5.7488646 -0.8155394 0.6299749 -0.9458767 -2.5538246 2.2083739 5.1146057 -3.5195148 -2.2233749 0.3551539 -0.1366535 -2.7792639 -0.7523574 -0.8642755 -2.5798709 -2.3095464 -2.3627650
200pmol max 1.5207481 2.7209140 2.0602758 -0.3758423 -0.1779857 -2.1284865 -0.4297874 5.2240199 5.3770232 0.0161123 1.1101593 1.0651086 -0.7232350 -1.3483859 1.1799089 -1.5199061 -0.5628205 1.1502570 6.6556177 5.6289970 6.3431905 -0.0161123 1.0727957 -0.6382337 -2.0869677 2.8151381 5.6912983 -2.9208223 -1.4198154 0.9018856 1.7437348 -2.0887997 0.5557834 -0.0738239 -1.0158409 -1.7187145 -0.5015723
200pmol range 0.6286959 3.5616990 0.6113249 0.5483203 1.8596261 0.4990269 1.0012621 0.5709082 0.5294318 0.4004740 0.6889996 0.3139684 0.7592797 1.1002145 0.7838817 0.5477278 0.4697697 0.5370829 0.6896469 0.6741157 0.5943259 0.7994271 0.4428208 0.3076430 0.4668569 0.6067642 0.5766927 0.5986925 0.8035595 0.5467318 1.8803883 0.6904642 1.3081408 0.7904516 1.5640300 0.5908319 1.8611927
200pmol skew -0.2304939 0.0277202 0.0511556 0.5485249 -0.4893530 0.5993218 0.1213269 -0.1655762 0.3232695 0.0151146 -0.3534406 0.3355272 0.2844003 -0.4142168 -0.1461126 -0.0447869 0.3722379 -0.1025752 0.1257074 0.1187445 0.0362543 0.0254412 0.0816792 -0.0432829 -0.3753531 0.1950853 0.1016950 -0.0782966 -0.2823102 -0.1652988 -0.6867482 -0.0496666 -0.4944364 -0.1640851 -0.5806949 0.4927092 -0.1727805
200pmol kurtosis -1.8715816 -2.3934838 -2.0603543 -1.8579454 -1.8464298 -1.7833417 -2.2996570 -1.9277409 -1.8613500 -2.0701536 -1.9324510 -2.0685048 -1.8979888 -1.8645279 -1.8715332 -2.0659894 -2.0306743 -1.8950212 -1.8904010 -1.8767332 -1.9010455 -1.9817762 -2.0657496 -2.0694059 -2.0013827 -1.8636760 -1.8906602 -2.3169268 -1.8941600 -2.2446394 -1.7348518 -2.1048953 -1.8034059 -2.2122722 -1.7703852 -1.8032402 -2.2355599
200pmol se 0.1296732 0.9181973 0.1309819 0.1292577 0.4030724 0.1107132 0.2520658 0.1187441 0.1102482 0.0859822 0.1480135 0.0749915 0.1588388 0.2339834 0.1605738 0.1175293 0.1117045 0.1103733 0.1417327 0.1380492 0.1220673 0.1674472 0.0951850 0.0660785 0.1054388 0.1244941 0.1183878 0.1453696 0.1678583 0.1321890 0.4412218 0.1500313 0.2781118 0.1841599 0.3391355 0.1255287 0.4482305
50pmol 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
50pmol mean 1.4882986 -1.5756840 0.7002420 -1.3230686 -0.8308088 -0.8313626 -0.9055283 3.6004797 4.5239268 0.1569678 0.1894755 1.1335623 -0.8062563 -2.6618971 0.5303625 -1.9591913 -0.8667673 1.1740093 4.9586671 3.8232457 4.7870003 1.1838709 0.9250217 -0.7460528 -1.9524060 2.7383775 5.6201911 -0.8788795 -1.6965592 -0.5631463 0.6757803 -2.9157401 0.0185304 -1.1873945 -1.3628512 -2.8387976 -2.2167837
50pmol sd 0.1654619 2.1853285 1.5432012 0.8046597 0.3527114 0.6743589 0.4562688 0.1970867 0.1797617 0.1339485 0.3044829 0.0878172 0.1353353 1.1295681 0.3016334 0.1247385 0.2892898 0.2074350 0.1841840 0.1994917 0.1539261 0.8064893 0.1225986 0.2990523 0.2842573 0.1555241 0.1833883 0.9745141 0.2475200 0.5119110 0.7008976 0.8962959 0.5490761 1.5988000 0.5800977 1.3138677 0.1827490
50pmol median 1.4796839 -1.7472227 1.4136299 -1.1173506 -0.7770172 -0.8972053 -0.7010233 3.6384927 4.5376269 0.1470047 0.0598001 1.1641047 -0.7875164 -2.3176735 0.6122013 -1.9898437 -1.0042273 1.1874884 4.9489444 3.8313659 4.7919450 0.8932836 0.8871143 -0.7722960 -2.0511823 2.7343238 5.6118669 -1.2140970 -1.6873857 -0.7795701 0.8761308 -2.5579410 0.0264428 -0.6085023 -1.5130281 -2.2626582 -2.2001640
50pmol trimmed 1.4882986 -1.5756840 0.7002420 -1.3230686 -0.8308088 -0.8313626 -0.9055283 3.6004797 4.5239268 0.1569678 0.1894755 1.1335623 -0.8062563 -2.6618971 0.5303625 -1.9591913 -0.8667673 1.1740093 4.9586671 3.8232457 4.7870003 1.1838709 0.9250217 -0.7460528 -1.9524060 2.7383775 5.6201911 -0.8788795 -1.6965592 -0.5631463 0.6757803 -2.9157401 0.0185304 -1.1873945 -1.3628512 -2.8387976 -2.2167837
50pmol mad 0.1974142 2.5284243 0.2252835 0.4015496 0.3149596 0.5429981 0.0769905 0.1718532 0.2085599 0.1559411 0.0886596 0.0463382 0.1061924 0.5052735 0.1758373 0.1012545 0.0305087 0.2424781 0.2161731 0.2434097 0.1893182 0.2944820 0.0796721 0.3411028 0.1540806 0.1919367 0.2211636 0.3307903 0.2833434 0.1546291 0.3903938 0.3104471 0.6157954 0.6070047 0.4171697 0.3157757 0.1828070
50pmol min 1.3361532 -3.4526216 -1.6053744 -2.4702967 -1.2905885 -1.5849506 -1.5868197 3.3453417 4.3411114 0.0418239 0.0000000 1.0090953 -0.9876086 -4.2987590 0.1019217 -2.0581389 -1.0248051 0.9560929 4.7788183 3.6330691 4.6370638 0.5802164 0.8333762 -1.0023667 -2.1551082 2.5916378 5.4523406 -1.6387928 -1.9818538 -0.8838660 -0.3248609 -4.2316052 -0.6292096 -3.5325733 -1.8530176 -4.7871833 -2.4453921
50pmol max 1.6576732 0.6443309 1.5790827 -0.5872764 -0.4786125 0.0539109 -0.6332468 3.7795919 4.6793421 0.2920380 0.6383018 1.1969443 -0.6623836 -1.7134826 0.7951258 -1.7989389 -0.4338096 1.3649676 5.1579612 3.9971817 4.9270473 2.3687002 1.0924818 -0.4372525 -1.5521514 2.8932246 5.8046900 0.5514687 -1.4296117 0.1904210 1.2757206 -2.3154730 0.6504456 0.0000000 -0.5723308 -2.0426906 -2.0214147
50pmol range 0.3215200 4.0969525 3.1844571 1.8830203 0.8119760 1.6388615 0.9535728 0.4342501 0.3382307 0.2502142 0.6383018 0.1878490 0.3252250 2.5852764 0.6932040 0.2592000 0.5909955 0.4088747 0.3791429 0.3641126 0.2899835 1.7884837 0.2591055 0.5651142 0.6029568 0.3015868 0.3523494 2.1902616 0.5522422 1.0742870 1.6005815 1.9161322 1.2796552 3.5325733 1.2806868 2.7444927 0.4239775
50pmol skew 0.0307207 0.0317523 -0.7325951 -0.5249413 -0.2736799 0.2156022 -0.7299384 -0.2898224 -0.0322072 0.0285345 0.6772215 -0.5372294 -0.2961458 -0.5964695 -0.5241931 0.2873983 0.7400574 -0.0439644 0.0494323 -0.0103183 -0.0133298 0.6585916 0.4287973 0.0396019 0.5166301 0.0149170 0.0238218 0.6513547 -0.0551286 0.6718983 -0.5449149 -0.6610022 -0.0262882 -0.6534707 0.4159054 -0.7013394 -0.1647526
50pmol kurtosis -2.3907126 -2.4009862 -1.7000215 -1.7900594 -2.0120773 -1.8674747 -1.7015632 -2.0805500 -2.4003668 -2.4046728 -1.7440044 -1.8680300 -1.8732196 -1.7677242 -1.8235898 -2.1189468 -1.6945391 -2.3740410 -2.3317379 -2.4254006 -2.4152774 -1.7442224 -1.9735578 -2.3920064 -1.8879715 -2.3990711 -2.4007329 -1.7401314 -2.1875424 -1.7484363 -1.8152991 -1.7563642 -2.0671088 -1.7510345 -1.9676310 -1.7243100 -2.0483042
50pmol se 0.0827310 1.0926643 0.7716006 0.4023299 0.1763557 0.3371794 0.2281344 0.0985434 0.0898809 0.0669743 0.1522415 0.0439086 0.0676677 0.5647841 0.1508167 0.0623692 0.1446449 0.1037175 0.0920920 0.0997459 0.0769630 0.4032446 0.0612993 0.1495262 0.1421286 0.0777621 0.0916942 0.4872571 0.1237600 0.2559555 0.3504488 0.4481479 0.2745381 0.7994000 0.2900489 0.6569338 0.0913745

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.

← Previous

Next →