shuffleData: Shuffles class labels to obtain random groups.
In PAA: PAA (Protein Array Analyzer)
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Shuffles class labels of an EList or EListRaw object randomly to
obtain two random groups (e.g. "A" and "B").
Usage
1
shuffleData(elist=NULL, n1=NULL, n2=NULL, label1="A", label2="B")
Arguments
elist
EList or EListRaw object (mandatory).
n1
sample size of random group 1 (mandatory).
n2
sample size of random group 2 (mandatory).
label1
class label of random group 1 (default: "A").
label2
class label of random group 2 (default: "B").
Details
Shuffles class labels of an EList or EListRaw object randomly to
obtain two random groups (e.g. "A" and "B").
Value
EList or EListRaw object with random groups.
Author(s)
Michael Turewicz, michael.turewicz@rub.de
Examples
1
2
3
cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
shuffleData(elist=elist, n1=20, n2=20, label1="A", label2="B")
Example output
Loading required package: Rcpp
An object of class "EListRaw"
$E
A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 A13 A14
[1,] 571 937 1200 8063 1164 870 3272 1166 1870 1154 780 475 830 865
[2,] 919 1671 1155 2655 1008 2644 989 14422 1422 952 1159 906 4491 4031
[3,] 595 563 476 867 751 613 564 651 599 626 628 372 625 475
[4,] 593 2089 1926 5023 781 1718 1045 11307 668 909 1676 903 3970 968
[5,] 878 1269 2514 4454 1857 2239 1378 2794 853 1072 1231 1043 7155 1171
A15 A16 A17 A18 A19 A20 B1 B2 B3 B4 B5 B6 B7 B8
[1,] 889 1235 1156 889 1239 635 1514 538 767 481 1143 761 444 822
[2,] 2232 6398 58246 880 931 998 11537 12172 2929 355 464 1771 519 2491
[3,] 615 728 238 646 987 531 583 557 523 296 253 457 395 624
[4,] 2468 2225 1753 944 1207 863 3664 2309 1718 981 632 1250 773 4161
[5,] 14929 3144 877 1653 1524 963 2207 914 2175 1333 19664 2549 864 1983
B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20
[1,] 1258 133 685 512 597 405 1238 908 979 538 482 1432
[2,] 1507 12458 1438 565 828 504 1857 902 6674 460 537 1620
[3,] 350 530 411 394 536 336 618 563 490 523 350 641
[4,] 968 954 681 1020 710 584 1371 1141 932 585 977 2466
[5,] 1737 1151 1026 5004 731 1467 1853 12901 2013 727 496 1778
9583 more rows ...
$Eb
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14 AD15 AD16
[1,] 55 67 84 129 90 65 54 61 65 91 98 85 75 73 85 77
[2,] 56 56 82 139 87 63 54 59 90 102 92 109 73 74 81 78
[3,] 60 63 77 148 81 72 55 60 274 321 105 92 80 71 77 77
[4,] 55 49 68 130 76 59 105 58 73 94 82 72 70 74 75 71
[5,] 65 58 71 131 76 66 75 67 67 93 78 80 72 75 79 76
AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7 NDC8 NDC9 NDC10
[1,] 297 81 78 78 86 76 74 96 74 78 69 74 79 67
[2,] 287 85 70 74 70 100 73 87 68 84 69 79 76 67
[3,] 303 89 73 76 85 195 74 102 72 80 249 83 87 70
[4,] 271 77 69 69 69 61 66 88 65 72 61 67 73 66
[5,] 279 75 73 69 75 63 73 85 70 74 70 73 75 74
NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19 NDC20
[1,] 102 71 74 66 64 61 71 61 64 59
[2,] 89 78 82 69 70 60 61 60 58 52
[3,] 86 70 76 83 81 71 84 57 67 51
[4,] 67 65 70 65 62 55 56 54 57 50
[5,] 66 71 70 68 66 70 63 54 59 52
9583 more rows ...
$targets
ArrayID FileName Group Batch
GSM734848_PA42314_-_AD16 A1 GSM734848_PA42314_-_AD16.gpr A Batch2
GSM734839_PA42122_-_AD7 A2 GSM734839_PA42122_-_AD7.gpr A Batch1
GSM735207_PA42029_-_CO17 A3 GSM735207_PA42029_-_CO17.gpr A Batch1
GSM734833_PA41992_-_AD1 A4 GSM734833_PA41992_-_AD1.gpr A Batch1
GSM734878_PA42125_-_AD47 A5 GSM734878_PA42125_-_AD47.gpr A Batch2
Date Array SerumID
GSM734848_PA42314_-_AD16 18.11.2010 42314 A1
GSM734839_PA42122_-_AD7 15.11.2010 42122 A2
GSM735207_PA42029_-_CO17 26.11.2010 42029 A3
GSM734833_PA41992_-_AD1 10.11.2010 41992 A4
GSM734878_PA42125_-_AD47 26.11.2010 42125 A5
35 more rows ...
$genes
Block Column Row Description
33 1 11 2 leucine-rich repeats and IQ motif containing 2 (LRRIQ2)
35 1 13 2 chromosome 5 open reading frame 3 (C5orf3)
37 1 15 2 chromosome 16 open reading frame 30 (C16orf30)
39 1 17 2 dynein, cytoplasmic 1, intermediate chain 1 (DYNC1I1)
41 1 19 2 Kruppel-like factor 3 (basic) (KLF3)
Name ID
33 Hs~Ref:NM_024548.2~uORF:IOH27601~RFU:10707.71 HA20251~B01R02C11
35 Hs~MGC:BC011414.1~uORF:IOH9720~RFU:29851.38 HA20251~B01R02C13
37 Hs~MGC:BC004932.1~uORF:IOH5521~RFU:9317.56 HA20251~B01R02C15
39 Hs~MGC:BC037854.1~uORF:IOH27633~RFU:35110.71 HA20251~B01R02C17
41 Hs~MGC:BC051687.1~uORF:IOH26538~RFU:41351.73 HA20251~B01R02C19
9583 more rows ...
$source
[1] "genepix.median"
$printer
$ngrid.r
[1] 12
$ngrid.c
[1] 4
$nspot.r
[1] 22
$nspot.c
[1] 22
$C
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14
[1,] 5755 5297 7755 7838 8450 8554 10226 9883 8588 9892 8653 9017 13317 10819
[2,] 6373 5479 7221 8250 8588 8223 9939 9897 9037 9535 7761 8511 14550 11095
[3,] 1322 2547 2593 2596 5297 1346 2315 905 1362 1430 2308 2028 1086 1297
[4,] 1310 3017 2695 2491 5206 1297 2285 898 1394 1406 2443 1825 1164 1351
[5,] 574 646 585 850 613 559 524 553 523 663 609 557 688 658
AD15 AD16 AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7
[1,] 9418 10066 12386 11201 10238 9704 10935 11278 10893 10204 8957 8603 7801
[2,] 9883 10126 12157 10584 9972 10110 12401 9873 10899 10075 9288 8200 7832
[3,] 3009 1396 1212 1900 1346 2183 2071 945 9613 1459 1307 1947 5247
[4,] 3043 1346 1188 1939 1275 2225 2064 820 9506 1534 1330 1943 5425
[5,] 616 564 939 622 478 517 747 629 551 617 569 513 498
NDC8 NDC9 NDC10 NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19
[1,] 8237 11441 11184 9283 10650 9534 10054 10425 8266 11860 11377 13856
[2,] 9182 11496 10011 8947 10068 9617 9976 9834 8350 11744 12954 14086
[3,] 1231 1534 10250 1131 706 1070 1824 2664 902 1831 2943 2358
[4,] 1164 1500 10489 1189 800 1219 1838 2681 859 1786 3007 4167
[5,] 613 630 555 502 544 560 505 633 485 580 545 747
NDC20
[1,] 11532
[2,] 11512
[3,] 3057
[4,] 3073
[5,] 606
4027 more rows ...
$Cb
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14 AD15 AD16
[1,] 49 52 65 64 82 59 48 55 56 81 107 77 69 63 68 68
[2,] 50 54 65 63 83 57 47 53 57 84 113 76 67 64 69 68
[3,] 49 55 63 58 78 55 45 51 57 84 109 72 67 64 70 69
[4,] 48 65 64 57 75 54 44 51 57 87 101 71 68 64 71 68
[5,] 50 60 65 83 79 57 46 52 57 89 92 71 68 64 70 67
AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7 NDC8 NDC9 NDC10
[1,] 321 74 71 65 62 63 66 85 71 75 59 64 67 65
[2,] 313 75 72 66 62 62 67 86 70 76 61 65 70 67
[3,] 306 75 70 65 61 60 66 82 65 74 60 63 70 66
[4,] 310 75 69 66 60 61 65 79 64 74 60 63 69 65
[5,] 308 74 69 66 60 61 65 80 63 74 61 63 70 63
NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19 NDC20
[1,] 59 64 64 50 53 50 54 55 54 60
[2,] 60 67 65 50 56 50 54 57 55 63
[3,] 59 63 64 49 57 50 53 56 56 57
[4,] 61 63 65 50 58 49 53 54 56 51
[5,] 63 63 65 51 58 49 53 53 55 49
4027 more rows ...
$cgenes
Block Column Row Description Name ID
1 1 1 1 Control AlexaAntiMouseAb HA20251~B01R01C01
2 1 2 1 Control AlexaAntiMouseAb HA20251~B01R01C02
3 1 3 1 Control ERa HA20251~B01R01C03
4 1 4 1 Control ERa HA20251~B01R01C04
5 1 5 1 Control HumanIgG1 HA20251~B01R01C05
4027 more rows ...
PAA documentation built on Nov. 8, 2020, 8:30 p.m.
R Package Documentation
Browse R Packages
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Description Usage Arguments Details Value Author(s) Examples
Description
Shuffles class labels of an EList or EListRaw object randomly to
obtain two random groups (e.g. "A" and "B").
Usage
1 | shuffleData(elist=NULL, n1=NULL, n2=NULL, label1="A", label2="B")
|
Arguments
elist |
|
n1 |
sample size of random group 1 (mandatory). |
n2 |
sample size of random group 2 (mandatory). |
label1 |
class label of random group 1 (default: |
label2 |
class label of random group 2 (default: |
Details
Shuffles class labels of an EList or EListRaw object randomly to
obtain two random groups (e.g. "A" and "B").
Value
EList or EListRaw object with random groups.
Author(s)
Michael Turewicz, michael.turewicz@rub.de
Examples
1 2 3 | cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
shuffleData(elist=elist, n1=20, n2=20, label1="A", label2="B")
|
Example output
Loading required package: Rcpp
An object of class "EListRaw"
$E
A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 A13 A14
[1,] 571 937 1200 8063 1164 870 3272 1166 1870 1154 780 475 830 865
[2,] 919 1671 1155 2655 1008 2644 989 14422 1422 952 1159 906 4491 4031
[3,] 595 563 476 867 751 613 564 651 599 626 628 372 625 475
[4,] 593 2089 1926 5023 781 1718 1045 11307 668 909 1676 903 3970 968
[5,] 878 1269 2514 4454 1857 2239 1378 2794 853 1072 1231 1043 7155 1171
A15 A16 A17 A18 A19 A20 B1 B2 B3 B4 B5 B6 B7 B8
[1,] 889 1235 1156 889 1239 635 1514 538 767 481 1143 761 444 822
[2,] 2232 6398 58246 880 931 998 11537 12172 2929 355 464 1771 519 2491
[3,] 615 728 238 646 987 531 583 557 523 296 253 457 395 624
[4,] 2468 2225 1753 944 1207 863 3664 2309 1718 981 632 1250 773 4161
[5,] 14929 3144 877 1653 1524 963 2207 914 2175 1333 19664 2549 864 1983
B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20
[1,] 1258 133 685 512 597 405 1238 908 979 538 482 1432
[2,] 1507 12458 1438 565 828 504 1857 902 6674 460 537 1620
[3,] 350 530 411 394 536 336 618 563 490 523 350 641
[4,] 968 954 681 1020 710 584 1371 1141 932 585 977 2466
[5,] 1737 1151 1026 5004 731 1467 1853 12901 2013 727 496 1778
9583 more rows ...
$Eb
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14 AD15 AD16
[1,] 55 67 84 129 90 65 54 61 65 91 98 85 75 73 85 77
[2,] 56 56 82 139 87 63 54 59 90 102 92 109 73 74 81 78
[3,] 60 63 77 148 81 72 55 60 274 321 105 92 80 71 77 77
[4,] 55 49 68 130 76 59 105 58 73 94 82 72 70 74 75 71
[5,] 65 58 71 131 76 66 75 67 67 93 78 80 72 75 79 76
AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7 NDC8 NDC9 NDC10
[1,] 297 81 78 78 86 76 74 96 74 78 69 74 79 67
[2,] 287 85 70 74 70 100 73 87 68 84 69 79 76 67
[3,] 303 89 73 76 85 195 74 102 72 80 249 83 87 70
[4,] 271 77 69 69 69 61 66 88 65 72 61 67 73 66
[5,] 279 75 73 69 75 63 73 85 70 74 70 73 75 74
NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19 NDC20
[1,] 102 71 74 66 64 61 71 61 64 59
[2,] 89 78 82 69 70 60 61 60 58 52
[3,] 86 70 76 83 81 71 84 57 67 51
[4,] 67 65 70 65 62 55 56 54 57 50
[5,] 66 71 70 68 66 70 63 54 59 52
9583 more rows ...
$targets
ArrayID FileName Group Batch
GSM734848_PA42314_-_AD16 A1 GSM734848_PA42314_-_AD16.gpr A Batch2
GSM734839_PA42122_-_AD7 A2 GSM734839_PA42122_-_AD7.gpr A Batch1
GSM735207_PA42029_-_CO17 A3 GSM735207_PA42029_-_CO17.gpr A Batch1
GSM734833_PA41992_-_AD1 A4 GSM734833_PA41992_-_AD1.gpr A Batch1
GSM734878_PA42125_-_AD47 A5 GSM734878_PA42125_-_AD47.gpr A Batch2
Date Array SerumID
GSM734848_PA42314_-_AD16 18.11.2010 42314 A1
GSM734839_PA42122_-_AD7 15.11.2010 42122 A2
GSM735207_PA42029_-_CO17 26.11.2010 42029 A3
GSM734833_PA41992_-_AD1 10.11.2010 41992 A4
GSM734878_PA42125_-_AD47 26.11.2010 42125 A5
35 more rows ...
$genes
Block Column Row Description
33 1 11 2 leucine-rich repeats and IQ motif containing 2 (LRRIQ2)
35 1 13 2 chromosome 5 open reading frame 3 (C5orf3)
37 1 15 2 chromosome 16 open reading frame 30 (C16orf30)
39 1 17 2 dynein, cytoplasmic 1, intermediate chain 1 (DYNC1I1)
41 1 19 2 Kruppel-like factor 3 (basic) (KLF3)
Name ID
33 Hs~Ref:NM_024548.2~uORF:IOH27601~RFU:10707.71 HA20251~B01R02C11
35 Hs~MGC:BC011414.1~uORF:IOH9720~RFU:29851.38 HA20251~B01R02C13
37 Hs~MGC:BC004932.1~uORF:IOH5521~RFU:9317.56 HA20251~B01R02C15
39 Hs~MGC:BC037854.1~uORF:IOH27633~RFU:35110.71 HA20251~B01R02C17
41 Hs~MGC:BC051687.1~uORF:IOH26538~RFU:41351.73 HA20251~B01R02C19
9583 more rows ...
$source
[1] "genepix.median"
$printer
$ngrid.r
[1] 12
$ngrid.c
[1] 4
$nspot.r
[1] 22
$nspot.c
[1] 22
$C
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14
[1,] 5755 5297 7755 7838 8450 8554 10226 9883 8588 9892 8653 9017 13317 10819
[2,] 6373 5479 7221 8250 8588 8223 9939 9897 9037 9535 7761 8511 14550 11095
[3,] 1322 2547 2593 2596 5297 1346 2315 905 1362 1430 2308 2028 1086 1297
[4,] 1310 3017 2695 2491 5206 1297 2285 898 1394 1406 2443 1825 1164 1351
[5,] 574 646 585 850 613 559 524 553 523 663 609 557 688 658
AD15 AD16 AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7
[1,] 9418 10066 12386 11201 10238 9704 10935 11278 10893 10204 8957 8603 7801
[2,] 9883 10126 12157 10584 9972 10110 12401 9873 10899 10075 9288 8200 7832
[3,] 3009 1396 1212 1900 1346 2183 2071 945 9613 1459 1307 1947 5247
[4,] 3043 1346 1188 1939 1275 2225 2064 820 9506 1534 1330 1943 5425
[5,] 616 564 939 622 478 517 747 629 551 617 569 513 498
NDC8 NDC9 NDC10 NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19
[1,] 8237 11441 11184 9283 10650 9534 10054 10425 8266 11860 11377 13856
[2,] 9182 11496 10011 8947 10068 9617 9976 9834 8350 11744 12954 14086
[3,] 1231 1534 10250 1131 706 1070 1824 2664 902 1831 2943 2358
[4,] 1164 1500 10489 1189 800 1219 1838 2681 859 1786 3007 4167
[5,] 613 630 555 502 544 560 505 633 485 580 545 747
NDC20
[1,] 11532
[2,] 11512
[3,] 3057
[4,] 3073
[5,] 606
4027 more rows ...
$Cb
AD1 AD2 AD3 AD4 AD5 AD6 AD7 AD8 AD9 AD10 AD11 AD12 AD13 AD14 AD15 AD16
[1,] 49 52 65 64 82 59 48 55 56 81 107 77 69 63 68 68
[2,] 50 54 65 63 83 57 47 53 57 84 113 76 67 64 69 68
[3,] 49 55 63 58 78 55 45 51 57 84 109 72 67 64 70 69
[4,] 48 65 64 57 75 54 44 51 57 87 101 71 68 64 71 68
[5,] 50 60 65 83 79 57 46 52 57 89 92 71 68 64 70 67
AD17 AD18 AD19 AD20 NDC1 NDC2 NDC3 NDC4 NDC5 NDC6 NDC7 NDC8 NDC9 NDC10
[1,] 321 74 71 65 62 63 66 85 71 75 59 64 67 65
[2,] 313 75 72 66 62 62 67 86 70 76 61 65 70 67
[3,] 306 75 70 65 61 60 66 82 65 74 60 63 70 66
[4,] 310 75 69 66 60 61 65 79 64 74 60 63 69 65
[5,] 308 74 69 66 60 61 65 80 63 74 61 63 70 63
NDC11 NDC12 NDC13 NDC14 NDC15 NDC16 NDC17 NDC18 NDC19 NDC20
[1,] 59 64 64 50 53 50 54 55 54 60
[2,] 60 67 65 50 56 50 54 57 55 63
[3,] 59 63 64 49 57 50 53 56 56 57
[4,] 61 63 65 50 58 49 53 54 56 51
[5,] 63 63 65 51 58 49 53 53 55 49
4027 more rows ...
$cgenes
Block Column Row Description Name ID
1 1 1 1 Control AlexaAntiMouseAb HA20251~B01R01C01
2 1 2 1 Control AlexaAntiMouseAb HA20251~B01R01C02
3 1 3 1 Control ERa HA20251~B01R01C03
4 1 4 1 Control ERa HA20251~B01R01C04
5 1 5 1 Control HumanIgG1 HA20251~B01R01C05
4027 more rows ...
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