Generate a wide data.frame from a SummarizedExperiment
get_df_wide.Rdget_df_wide generate a wide data.frame from a SummarizedExperiment.
Value
A data.frame object containing all data in a wide format(combine the assay and rowData), where each row represents a protein/gene.
Examples
# Load example
data(Silicosis_pg)
data_unique <- make_unique(Silicosis_pg, "Gene.names", "Protein.IDs", delim = ";")
# Make SummarizedExperiment
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols, mode = "delim", sep = "_")
# Filter and normalize
filt <- filter_se(se, thr = 0, fraction = 0.4, filter_formula = ~ Reverse != "+" & Potential.contaminant!="+")
#> filter base on missing number is <= 0 in at least one condition.
#> filter base on missing number fraction < 0.4 in each row
#> filter base on giving formula
norm <- normalize_vsn(filt)
#> vsn2: 8762 x 20 matrix (1 stratum).
#> Please use 'meanSdPlot' to verify the fit.
imputed <- impute(norm, fun = "MinDet")
#> Imputing along margin 2 (samples/columns).
diff <- test_diff(imputed,type = "control", control = "PBS")
#> Tested contrasts: W10_vs_PBS, W2_vs_PBS, W4_vs_PBS, W6_vs_PBS, W9_vs_PBS
#> Strimmer's qvalue(t)
dep <- add_rejections(diff)
get_df_wide(dep)
#> name PBS_1 PBS_2 PBS_3 PBS_4 W10_2 W10_4 W2_1
#> 1 4931429I11Rik 28.70045 24.93761 29.75342 29.95957 24.89231 28.23119 30.34856
#> 2 4932418E24Rik 27.78676 27.95045 28.11689 28.63062 27.92583 28.32200 27.91089
#> 3 9230110C19Rik 28.15309 27.59883 27.18844 27.67702 27.80568 28.01911 27.81927
#> 4 A0A0B4J1G0 25.01261 24.93761 25.11992 24.96369 27.32584 26.73893 23.79471
#> 5 A2AG58 28.34999 27.51432 25.00725 28.70948 28.01023 27.44449 28.63363
#> 6 A2m 34.57332 34.72135 35.78446 35.04418 33.46302 33.85551 33.14775
#> 7 A3KGF9 29.64549 29.22066 29.24076 29.72597 28.89847 29.03256 28.89834
#> 8 A6H630 28.51091 29.00241 29.09496 28.86264 29.21694 29.19137 29.02402
#> 9 Aaas 28.44612 28.44058 28.85120 28.68186 28.96055 28.89964 28.91826
#> 10 Aacs 30.43128 30.47401 30.28250 30.60539 30.79143 31.06079 30.76782
#> W2_3 W2_4 W2_5 W4_2 W4_3 W4_4 W4_5 W6_2
#> 1 29.50451 29.03613 29.55282 28.68068 29.31367 29.16450 29.10021 28.38552
#> 2 27.05942 27.28252 27.08586 28.32345 28.56645 28.04732 28.61185 28.12572
#> 3 27.37634 27.44095 27.58823 27.83905 28.19786 28.05611 27.53541 28.11495
#> 4 27.14472 26.21215 26.60410 26.01617 24.74135 26.51245 26.05723 25.89587
#> 5 28.43678 28.81267 28.30759 27.82674 28.02356 27.61256 24.86456 27.98525
#> 6 34.31248 33.46066 33.24186 33.19310 32.74648 33.58896 33.32027 33.71811
#> 7 28.71770 28.71744 28.71441 28.63737 28.89839 28.22483 29.30059 28.87607
#> 8 28.96318 29.14451 29.06034 29.00653 29.05851 29.29631 29.39051 29.24155
#> 9 29.05142 28.83850 28.55392 29.07915 28.76030 29.06208 28.90197 29.14340
#> 10 30.96020 30.70033 30.81449 30.80066 30.49656 30.68210 30.43653 30.63227
#> W6_3 W6_4 W6_6 W9_2 W9_4 Protein.IDs
#> 1 24.85031 24.74397 24.78682 27.19517 24.84699 E9Q793
#> 2 27.52801 27.60662 27.82703 28.25101 27.56389 Q8C5V8
#> 3 27.49192 27.90190 28.09850 28.01374 27.10166 Q8CC70
#> 4 26.76816 26.72821 26.84339 26.52089 27.00605 A0A0B4J1G0
#> 5 27.78401 27.89912 27.62169 28.38426 24.84699 A2AG58
#> 6 33.75012 34.04199 33.46282 34.35617 33.56346 Q61838
#> 7 28.26034 28.59259 28.58033 28.58008 28.71798 A3KGF9
#> 8 29.30918 29.17283 29.50891 29.01680 29.29224 A6H630
#> 9 29.10231 28.91989 28.32318 28.88143 29.08772 P58742
#> 10 30.77801 30.88343 30.89412 29.71736 30.40523 Q9D2R0
#> Majority.protein.IDs Peptide.counts..all. Peptide.counts..razor.unique.
#> 1 E9Q793 7 7
#> 2 Q8C5V8 15 15
#> 3 Q8CC70 14 14
#> 4 A0A0B4J1G0 3 3
#> 5 A2AG58 10 10
#> 6 Q61838 58 58
#> 7 A3KGF9 14 14
#> 8 A6H630 15 15
#> 9 P58742 12 12
#> 10 Q9D2R0 20 20
#> Peptide.counts..unique.
#> 1 7
#> 2 15
#> 3 14
#> 4 3
#> 5 10
#> 6 56
#> 7 14
#> 8 15
#> 9 12
#> 10 20
#> Protein.names
#> 1
#> 2
#> 3
#> 4
#> 5 Uncharacterized protein CXorf23 homolog
#> 6 Alpha-2-macroglobulin;Alpha-2-macroglobulin 165 kDa subunit;Alpha-2-macroglobulin 35 kDa subunit
#> 7 Uncharacterized protein C15orf52 homolog
#> 8 UPF0364 protein C6orf211 homolog
#> 9 Aladin
#> 10 Acetoacetyl-CoA synthetase
#> Gene.names
#> 1 4931429I11Rik
#> 2 4932418E24Rik
#> 3 9230110C19Rik
#> 4
#> 5
#> 6 A2m
#> 7
#> 8
#> 9 Aaas
#> 10 Aacs
#> Fasta.headers
#> 1 >E9Q793 Jhy protein OS=Mus musculus OX=10090 GN=Jhy PE=1 SV=1
#> 2 >Q8C5V8 Coiled-coil domain-containing protein 187 OS=Mus musculus OX=10090 GN=Ccdc187 PE=2 SV=1
#> 3 >Q8CC70 Cilia- and flagella-associated protein 300 OS=Mus musculus OX=10090 GN=Cfap300 PE=2 SV=1
#> 4 >A0A0B4J1G0 Low affinity immunoglobulin gamma Fc region receptor IV OS=Mus musculus OX=10090 GN=Fcgr4 PE=1 SV=1
#> 5 >A2AG58 BCLAF1 and THRAP3 family member 3 OS=Mus musculus OX=10090 GN=Bclaf3 PE=1 SV=1
#> 6 >Q61838 Pregnancy zone protein OS=Mus musculus OX=10090 GN=Pzp PE=1 SV=3
#> 7 >A3KGF9 Coiled-coil domain-containing protein 9B OS=Mus musculus OX=10090 GN=Ccdc9b PE=1 SV=1
#> 8 >A6H630 Damage-control phosphatase ARMT1 OS=Mus musculus OX=10090 GN=Armt1 PE=1 SV=1
#> 9 >P58742 Aladin OS=Mus musculus OX=10090 GN=Aaas PE=1 SV=1
#> 10 >Q9D2R0 Acetoacetyl-CoA synthetase OS=Mus musculus OX=10090 GN=Aacs PE=1 SV=1
#> Number.of.proteins Peptides Razor...unique.peptides Unique.peptides
#> 1 1 7 7 7
#> 2 1 15 15 15
#> 3 1 14 14 14
#> 4 1 3 3 3
#> 5 1 10 10 10
#> 6 1 58 58 56
#> 7 1 14 14 14
#> 8 1 15 15 15
#> 9 1 12 12 12
#> 10 1 20 20 20
#> iBAQ.PBS_1 iBAQ.PBS_2 iBAQ.PBS_3 iBAQ.PBS_4 iBAQ.W10_2 iBAQ.W10_4 iBAQ.W2_1
#> 1 770730 31396 600530 73060000 830230 44453000 101360000
#> 2 4431600 5686400 7911100 7356500 10941000 10549000 11432000
#> 3 14583000 14419000 13432000 10295000 18398000 21712000 27832000
#> 4 1371700 0 2541900 214960 15586000 7950500 1476700
#> 5 986190 2576800 925390 1450600 70833000 35955000 1985800
#> 6 499830000 737940000 1818300000 670060000 295580000 368630000 296600000
#> 7 52617000 40555000 54628000 51936000 29640000 30177000 60573000
#> 8 21935000 23175000 25195000 21827000 41439000 36086000 50951000
#> 9 17838000 21573000 27395000 17450000 38805000 28214000 51485000
#> 10 50426000 93386000 68973000 37103000 65184000 87003000 114290000
#> iBAQ.W2_3 iBAQ.W2_4 iBAQ.W2_5 iBAQ.W4_2 iBAQ.W4_3 iBAQ.W4_4 iBAQ.W4_5
#> 1 64003000 52267000 48484000 1762100 924580 1383500 2082500
#> 2 5231400 6075000 4720600 19217000 19552000 14223000 16121000
#> 3 16129000 16620000 22499000 36050000 29538000 17628000 18354000
#> 4 14318000 8884100 9379500 11780000 3277000 11987000 7910500
#> 5 4812900 2590500 3013700 1383500 1824300 1132000 870670
#> 6 761380000 374630000 249670000 340750000 225400000 500280000 216580000
#> 7 31654000 61950000 53766000 58985000 77566000 36290000 45419000
#> 8 46976000 54470000 49546000 53063000 64049000 72514000 54845000
#> 9 47803000 43782000 39204000 71399000 41772000 44288000 34274000
#> 10 125590000 122650000 118750000 151120000 127440000 141570000 83758000
#> iBAQ.W6_2 iBAQ.W6_3 iBAQ.W6_4 iBAQ.W6_6 iBAQ.W9_2 iBAQ.W9_4
#> 1 1271700 380510 391260 741790 907870 222640
#> 2 13346000 5071000 4442200 6194200 13517000 8740800
#> 3 19766000 18147000 19754000 27357000 30529000 23216000
#> 4 9806000 11549000 56719000 13334000 9592600 17502000
#> 5 1906800 3721400 1907400 1398100 73530000 37570000
#> 6 356200000 397190000 429730000 393690000 529520000 528520000
#> 7 65303000 27033000 31609000 35756000 27126000 25407000
#> 8 36438000 38266000 30553000 40028000 39247000 67352000
#> 9 40420000 27954000 34855000 32843000 33375000 48230000
#> 10 84367000 89265000 84252000 104790000 43751000 102510000
#> Only.identified.by.site Reverse Potential.contaminant ID imputed
#> 1 E9Q793 TRUE
#> 2 Q8C5V8 FALSE
#> 3 Q8CC70 FALSE
#> 4 A0A0B4J1G0 TRUE
#> 5 A2AG58 TRUE
#> 6 Q61838 FALSE
#> 7 A3KGF9 FALSE
#> 8 A6H630 FALSE
#> 9 P58742 FALSE
#> 10 Q9D2R0 FALSE
#> num_NAs W10_vs_PBS_CI.L W10_vs_PBS_CI.R W10_vs_PBS_diff W10_vs_PBS_p.adj
#> 1 6 -4.483048131 0.931022178 -1.776012976 0.9893567
#> 2 0 -0.592377635 0.597846171 0.002734268 0.9943193
#> 3 0 -0.323212323 0.839310659 0.258049168 0.9915779
#> 4 3 0.637957874 3.409900613 2.023929244 0.9659200
#> 5 3 -1.784762674 2.448961842 0.332099584 0.9935751
#> 6 0 -2.126200751 -0.616927987 -1.371564369 0.9345667
#> 7 0 -0.983815632 -0.001594425 -0.492705029 0.9833366
#> 8 0 0.005283889 0.667559841 0.336421865 0.9830344
#> 9 0 -0.102208905 0.752516398 0.325153747 0.9879197
#> 10 0 0.124693499 0.830942120 0.477817809 0.9715452
#> W10_vs_PBS_p.val W10_vs_PBS_t.stastic W2_vs_PBS_CI.L W2_vs_PBS_CI.R
#> 1 0.183605084 -1.388686131 -0.93754041 3.4830295
#> 2 0.992358596 0.009725103 -1.27241072 -0.3005971
#> 3 0.361090316 0.939686032 -0.57274463 0.3764514
#> 4 0.006888739 3.090956733 -0.20117708 2.0621047
#> 5 0.744067529 0.332068432 -0.57600225 2.8808193
#> 6 0.001380892 -3.847071999 -2.10630022 -0.8739842
#> 7 0.049343170 -2.123535584 -1.09723720 -0.2952569
#> 8 0.046847156 2.150438780 -0.09009276 0.4506533
#> 9 0.126486871 1.610438174 -0.11335291 0.5845274
#> 10 0.011087299 2.864089431 0.07408847 0.6507381
#> W2_vs_PBS_diff W2_vs_PBS_p.adj W2_vs_PBS_p.val W2_vs_PBS_t.stastic
#> 1 1.27274454 0.9746468 2.402457e-01 1.2188348
#> 2 -0.78650389 0.9149317 3.385014e-03 -3.4260975
#> 3 -0.09814661 0.9813451 6.673280e-01 -0.4377249
#> 4 0.93046380 0.9677531 1.006268e-01 1.7403745
#> 5 1.15240855 0.9723870 1.769581e-01 1.4112741
#> 6 -1.49014219 0.7265995 9.714713e-05 -5.1190275
#> 7 -0.69624707 0.8996252 1.991209e-03 -3.6752049
#> 8 0.18028026 0.9723860 1.769342e-01 1.4113563
#> 9 0.23558723 0.9721627 1.718612e-01 1.4290673
#> 10 0.36241326 0.9471235 1.689648e-02 2.6605655
#> W4_vs_PBS_CI.L W4_vs_PBS_CI.R W4_vs_PBS_diff W4_vs_PBS_p.adj W4_vs_PBS_p.val
#> 1 -1.483282456 2.9372874 0.7270025 0.9862680 4.961023e-01
#> 2 -0.219818561 0.7519951 0.2660883 0.9829668 2.631035e-01
#> 3 -0.221831081 0.7273650 0.2527669 0.9832323 2.759232e-01
#> 4 -0.308296912 1.9549849 0.8233440 0.9792178 1.427358e-01
#> 5 -2.041812442 1.4150091 -0.3134016 0.9879364 7.060839e-01
#> 6 -2.434783663 -1.2024676 -1.8186256 0.4209380 1.068546e-05
#> 7 -1.093917709 -0.2919375 -0.6929276 0.9106033 2.066958e-03
#> 8 0.049862647 0.5906087 0.3202357 0.9623430 2.311004e-02
#> 9 -0.003004205 0.6948761 0.3459359 0.9711607 5.178081e-02
#> 10 -0.132655769 0.4439938 0.1556690 0.9831038 2.696210e-01
#> W4_vs_PBS_t.stastic W6_vs_PBS_CI.L W6_vs_PBS_CI.R W6_vs_PBS_diff
#> 1 0.6962088 -4.85639066 -0.4358208 -2.6461057
#> 2 1.1591098 -0.83524036 0.1365733 -0.3493335
#> 3 1.1273174 -0.22712111 0.7220749 0.2474769
#> 4 1.5400135 0.41881151 2.6820933 1.5504524
#> 5 -0.3838011 -1.30115300 2.1556686 0.4272578
#> 6 -6.2474539 -1.90372843 -0.6714124 -1.2875704
#> 7 -3.6576827 -1.28187668 -0.4798964 -0.8808866
#> 8 2.5070224 0.17001235 0.7107584 0.4403854
#> 9 2.0984402 -0.08168201 0.6161983 0.2672581
#> 10 1.1428048 0.06033873 0.6369883 0.3486635
#> W6_vs_PBS_p.adj W6_vs_PBS_p.val W6_vs_PBS_t.stastic W9_vs_PBS_CI.L
#> 1 0.9752893 0.0218790438 -2.5340243 -5.02371683
#> 2 0.9852016 0.1472291829 -1.5217353 -0.80884175
#> 3 0.9876437 0.2857340175 1.1037243 -0.67790203
#> 4 0.9694513 0.0102861922 2.9000245 0.36904631
#> 5 0.9900946 0.6078496489 0.5232327 -2.89649630
#> 6 0.9149359 0.0004084331 -4.4231405 -1.82565103
#> 7 0.8993172 0.0002544939 -4.6498416 -1.30030071
#> 8 0.9569433 0.0032333508 3.4476358 -0.04434635
#> 9 0.9845116 0.1241516312 1.6211823 -0.04772833
#> 10 0.9749315 0.0207696861 2.5596252 -0.74012367
#> W9_vs_PBS_CI.R W9_vs_PBS_diff W9_vs_PBS_p.adj W9_vs_PBS_p.val
#> 1 0.39035348 -2.31668167 0.9209222 0.088530728
#> 2 0.38138205 -0.21372985 0.9536745 0.457995552
#> 3 0.48462095 -0.09664054 0.9609172 0.729407318
#> 4 3.14098905 1.75501768 0.8644724 0.016225666
#> 5 1.33722821 -0.77963405 0.9532747 0.446816408
#> 6 -0.31637826 -1.07101465 0.8315420 0.008271400
#> 7 -0.31807950 -0.80919010 0.7879762 0.002969802
#> 8 0.61792960 0.28679163 0.9199272 0.085092831
#> 9 0.80699697 0.37963432 0.9177157 0.078055722
#> 10 -0.03387504 -0.38699936 0.8926160 0.033632498
#> W9_vs_PBS_t.stastic W10_vs_PBS_significant W2_vs_PBS_significant
#> 1 -1.8114416 FALSE FALSE
#> 2 -0.7601834 FALSE FALSE
#> 3 -0.3519165 FALSE FALSE
#> 4 2.6802734 FALSE FALSE
#> 5 -0.7795609 FALSE FALSE
#> 6 -3.0040664 FALSE FALSE
#> 7 -3.4875714 FALSE FALSE
#> 8 1.8331978 FALSE FALSE
#> 9 1.8802723 FALSE FALSE
#> 10 -2.3197142 FALSE FALSE
#> W4_vs_PBS_significant W6_vs_PBS_significant W9_vs_PBS_significant
#> 1 FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE
#> 3 FALSE FALSE FALSE
#> 4 FALSE FALSE FALSE
#> 5 FALSE FALSE FALSE
#> 6 FALSE FALSE FALSE
#> 7 FALSE FALSE FALSE
#> 8 FALSE FALSE FALSE
#> 9 FALSE FALSE FALSE
#> 10 FALSE FALSE FALSE
#> significant
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> 5 FALSE
#> 6 FALSE
#> 7 FALSE
#> 8 FALSE
#> 9 FALSE
#> 10 FALSE
#> [ reached 'max' / getOption("max.print") -- omitted 8752 rows ]