jaccard.test.bootstrap: Compute p-value using the bootstrap procedure
In jaccard: Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients
Description
Usage
Arguments
Value
Examples
View source: R/jaccard.test.bootstrap.R
Description
Compute statistical significance of Jaccard/Tanimoto similarity coefficients.
Usage
1
2
Arguments
x
a binary vector (e.g., fingerprint)
y
a binary vector (e.g., fingerprint)
px
probability of successes in x (optional)
py
probability of successes in y (optional)
verbose
whether to print progress messages
fix
whether to fix (i.e., not resample) x and/or y
B
a total bootstrap iteration
seed
a seed for a random number generator
Value
jaccard.test.bootstrap returns a list consisting of
statistics
centered Jaccard/Tanimoto similarity coefficient
pvalue
p-value
expectation
expectation
Examples
1
2
3
4
set.seed(1234)
x = rbinom(100,1,.5)
y = rbinom(100,1,.5)
jaccard.test.bootstrap(x,y,B=500)
Example output
Bootstrap Procedures :
50 100 150 200 250 300 350 400 450 500 $statistics
[1] -0.02460145
$statistics.null
[1] -0.0489180408 0.0044296788 0.0308631787 -0.0112775240 -0.0498575499
[6] 0.0807138179 -0.0652350571 0.0191649555 -0.0263461114 -0.0436781609
[11] 0.0026790108 0.0000000000 -0.0674151311 -0.0317304241 -0.0207655142
[16] -0.0498575499 0.0677795031 0.0276833414 0.0368923112 -0.0035064574
[21] -0.0009072658 0.0276833414 -0.0395869191 0.0424255297 0.0390355913
[26] 0.0174825175 -0.0207655142 -0.0789036545 -0.0609528487 0.0379442982
[31] -0.0089749646 0.0276833414 -0.0207402180 0.0055476529 -0.0674151311
[36] 0.0256192450 -0.0489180408 -0.0581945229 -0.0765785938 0.0354251012
[41] -0.0652350571 0.0795470497 -0.0149786469 -0.0149786469 0.0613074252
[46] 0.0379442982 -0.0674151311 -0.0282605410 -0.0071239718 -0.0721366479
[51] -0.1085311969 0.0174390102 0.0174808406 -0.0131141808 0.0073381465
[56] -0.0226696259 -0.0341683778 -0.0457642516 -0.0246014493 0.0453050786
[61] 0.0191649555 0.0394657976 -0.0263461114 -0.1013346163 0.0986445415
[66] 0.0613074252 -0.0146985962 0.0140252454 -0.0900866813 -0.0560704356
[71] -0.0539728132 0.0482624005 0.0308631787 0.0954213982 -0.0489180408
[76] 0.0240471513 -0.0395869191 0.0548935842 -0.0247216731 -0.0089749646
[81] 0.0409593592 -0.0247216731 0.0243882326 -0.0361925511 0.0240471513
[86] -0.0878012048 0.0190767934 -0.0035064574 0.0095154156 -0.0718513291
[91] 0.0108323407 0.0108323407 0.0061524144 -0.0375820310 0.0783546864
[96] 0.0758901198 -0.0017394829 0.0609284988 -0.0131141808 -0.0017394829
[101] 0.0452778988 -0.0188890000 -0.0531294881 -0.0149786469 -0.0856836006
[106] -0.0108543417 0.0613074252 -0.0246014493 0.0292874396 0.0496987952
[111] 0.0733137830 0.0677795031 -0.0539728132 0.0292874396 0.0086189206
[116] -0.0765785938 0.0818557266 0.0191649555 -0.0510104831 -0.0053012048
[121] 0.0867139959 -0.0089749646 0.0409593592 -0.0265610438 -0.0035064574
[126] -0.0027433479 -0.0424279105 0.0276833414 0.0000000000 0.1523107355
[131] -0.0436781609 0.0703239519 0.0009001153 -0.0468523724 0.0348153376
[136] 0.0256192450 0.0256192450 -0.0035064574 0.0271644333 -0.0341683778
[141] -0.0108543417 0.0298992890 -0.0560704356 0.0703239519 -0.0721366479
[146] -0.0369278973 -0.0457642516 0.0240471513 -0.0053012048 -0.0375820310
[151] -0.0428018076 -0.0027433479 -0.0609528487 0.0108323407 0.0276833414
[156] 0.0529610014 -0.0302023558 0.0467980296 -0.0089749646 -0.0833042596
[161] -0.0168710805 0.0339315128 0.0379442982 0.0009001153 0.0315683056
[166] 0.0308631787 0.0157677185 0.0453050786 0.0771359700 0.0026790108
[171] 0.0394657976 0.0108323407 0.0544231807 -0.0436781609 0.0111564042
[176] 0.0158613373 0.0125366330 0.0482624005 -0.0468523724 0.0409593592
[181] 0.0026790108 -0.0547273841 0.0174825175 0.0292874396 -0.0428018076
[186] -0.0282605410 0.0276833414 -0.0603448276 0.0529610014 -0.0225988701
[191] -0.0521809270 -0.0361925511 -0.0285484057 -0.0560704356 -0.0207655142
[196] -0.0457642516 0.0276833414 -0.0071239718 -0.0382440232 -0.0408169680
[201] 0.0044296788 0.0240471513 0.0453050786 -0.0265610438 0.0073381465
[206] -0.0766935895 -0.0609528487 0.0771359700 0.0174808406 0.0363943215
[211] -0.0403225806 -0.0489180408 0.0240471513 0.0840677966 -0.0134232320
[216] -0.0027433479 -0.0743450390 0.0243882326 0.0900813854 -0.0302023558
[221] -0.0361925511 -0.0552747525 0.0061524144 0.0758901198 -0.0149786469
[226] -0.0089749646 -0.0721366479 -0.0108543417 -0.0367726584 0.0066895572
[231] 0.1065699007 0.0226963618 0.0208204399 -0.0053012048 0.1403770767
[236] -0.0149786469 0.0409593592 0.0637566081 0.0986445415 0.0033977556
[241] -0.0302023558 0.0911537350 0.0191649555 0.0758901198 -0.0321716293
[246] -0.0510104831 0.0224476969 -0.0375820310 0.0142128408 -0.0356043522
[251] -0.0341683778 -0.0539728132 0.0018787251 -0.0966453136 0.0090996169
[256] -0.0187915885 0.0026790108 -0.0498575499 -0.0187915885 0.0260504202
[261] -0.0702179177 0.0942928040 -0.0531294881 -0.0436781609 -0.0265610438
[266] 0.0703239519 -0.0071239718 -0.0375820310 0.0271644333 0.0037279048
[271] 0.0438648590 0.0224476969 -0.0674151311 0.0009001153 -0.0788367979
[276] 0.0482624005 -0.0531294881 0.1403770767 -0.0356043522 0.0373909332
[281] -0.0246014493 0.0090996169 0.0142128408 -0.0510104831 0.0613074252
[286] -0.0046082949 0.0878623188 0.0467980296 0.0174825175 -0.0765785938
[291] 0.0018787251 0.0348153376 0.0409593592 -0.0059322034 0.0292874396
[296] -0.0009072658 -0.0089749646 0.0276833414 0.0795470497 -0.0510104831
[301] 0.0715570836 -0.0071239718 0.0394657976 0.0613074252 -0.0603448276
[306] -0.0131141808 -0.0246014493 -0.0302023558 -0.0071239718 0.0348153376
[311] 0.0558560192 -0.0356043522 -0.0317304241 0.0108323407 -0.0166634744
[316] 0.0637566081 -0.0112775240 -0.0656660413 0.0482624005 0.0379442982
[321] 0.0037279048 0.0226963618 -0.0457642516 -0.0187915885 -0.0669490854
[326] -0.0263461114 0.0260504202 -0.0408169680 -0.0027433479 0.0379442982
[331] 0.0437829470 0.0208204399 -0.0625210084 0.0108323407 -0.0076867914
[336] -0.0489180408 -0.0382440232 0.0409593592 0.0157677185 -0.1109688519
[341] -0.0227169468 -0.0168710805 -0.0149786469 -0.0265610438 0.0044296788
[346] -0.0285484057 -0.0112775240 -0.0302023558 0.0026790108 -0.0834244649
[351] 0.0140252454 0.0363943215 -0.0168710805 -0.0468523724 -0.0046082949
[356] -0.0467170478 -0.0603448276 0.0276833414 -0.0149786469 0.0108323407
[361] 0.0332068311 0.0332068311 0.0061524144 -0.0428018076 0.0383336530
[366] 0.0226963618 -0.0207655142 -0.0027433479 -0.1265233623 0.0157677185
[371] 0.0090996169 0.0308631787 -0.0652350571 -0.0053012048 -0.0436781609
[376] 0.0157677185 -0.0448136082 0.0174825175 -0.0989785044 -0.0539728132
[381] 0.0529610014 0.0276833414 -0.0089749646 0.1396910248 0.0208204399
[386] 0.0000000000 -0.0131141808 0.0140252454 -0.0630808697 0.0783546864
[391] -0.0521809270 -0.0285484057 -0.0166634744 0.0026790108 -0.0718513291
[396] -0.0263461114 0.0256192450 -0.0321716293 0.0044296788 0.0055476529
[401] -0.0674151311 0.0690649924 0.0422310413 0.0677795031 0.0090996169
[406] -0.0166634744 -0.0187915885 0.0558560192 -0.0574458683 0.0190767934
[411] 0.0379442982 -0.0356043522 -0.0970839260 0.0240471513 0.0467980296
[416] -0.1030789826 -0.0168710805 0.0453050786 0.0524900713 -0.0321716293
[421] 0.0878623188 -0.0112775240 -0.0478400296 -0.0094684743 -0.0071239718
[426] 0.0271644333 -0.0428018076 0.0409593592 0.0572601936 -0.0855402456
[431] -0.0560704356 -0.0718513291 0.0394657976 -0.0321716293 0.0260504202
[436] -0.0652350571 0.0271644333 -0.0009072658 -0.0168710805 -0.0094684743
[441] -0.0112775240 -0.0265610438 0.0437829470 -0.0321716293 0.0453050786
[446] 0.0739485883 -0.0046082949 0.0467980296 -0.0336538462 0.0044296788
[451] -0.0468523724 -0.0321716293 0.0018787251 0.0511078180 -0.0035064574
[456] -0.0721366479 0.0224476969 -0.0395869191 0.0224476969 0.0243882326
[461] -0.0246014493 -0.0035064574 0.0453050786 -0.0084251317 -0.0416189931
[466] 0.0424255297 -0.0302023558 -0.0457642516 -0.0302023558 0.0308631787
[471] 0.0394657976 -0.0017394829 -0.0674151311 -0.0089749646 0.0315683056
[476] -0.0094684743 0.0260504202 0.0108323407 0.0931354698 0.0095154156
[481] 0.0324110390 0.0044296788 -0.0468523724 0.0073381465 -0.0531294881
[486] -0.0207655142 0.0174808406 0.0292874396 -0.0346758968 -0.0207402180
[491] 0.0026790108 -0.0089749646 -0.0552747525 -0.0539728132 -0.0603448276
[496] 0.0586363766 0.0174808406 0.0599852344 0.0073381465 -0.0382440232
$pvalue
[1] 0.63
$expectation
[1] 0.3179348
jaccard documentation built on May 2, 2019, 12:51 p.m.
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Description Usage Arguments Value Examples
View source: R/jaccard.test.bootstrap.R
Description
Compute statistical significance of Jaccard/Tanimoto similarity coefficients.
Usage
1 2 |
Arguments
x |
a binary vector (e.g., fingerprint) |
y |
a binary vector (e.g., fingerprint) |
px |
probability of successes in |
py |
probability of successes in |
verbose |
whether to print progress messages |
fix |
whether to fix (i.e., not resample) |
B |
a total bootstrap iteration |
seed |
a seed for a random number generator |
Value
jaccard.test.bootstrap returns a list consisting of
statistics |
centered Jaccard/Tanimoto similarity coefficient |
pvalue |
p-value |
expectation |
expectation |
Examples
1 2 3 4 | set.seed(1234)
x = rbinom(100,1,.5)
y = rbinom(100,1,.5)
jaccard.test.bootstrap(x,y,B=500)
|
Example output
Bootstrap Procedures :
50 100 150 200 250 300 350 400 450 500 $statistics
[1] -0.02460145
$statistics.null
[1] -0.0489180408 0.0044296788 0.0308631787 -0.0112775240 -0.0498575499
[6] 0.0807138179 -0.0652350571 0.0191649555 -0.0263461114 -0.0436781609
[11] 0.0026790108 0.0000000000 -0.0674151311 -0.0317304241 -0.0207655142
[16] -0.0498575499 0.0677795031 0.0276833414 0.0368923112 -0.0035064574
[21] -0.0009072658 0.0276833414 -0.0395869191 0.0424255297 0.0390355913
[26] 0.0174825175 -0.0207655142 -0.0789036545 -0.0609528487 0.0379442982
[31] -0.0089749646 0.0276833414 -0.0207402180 0.0055476529 -0.0674151311
[36] 0.0256192450 -0.0489180408 -0.0581945229 -0.0765785938 0.0354251012
[41] -0.0652350571 0.0795470497 -0.0149786469 -0.0149786469 0.0613074252
[46] 0.0379442982 -0.0674151311 -0.0282605410 -0.0071239718 -0.0721366479
[51] -0.1085311969 0.0174390102 0.0174808406 -0.0131141808 0.0073381465
[56] -0.0226696259 -0.0341683778 -0.0457642516 -0.0246014493 0.0453050786
[61] 0.0191649555 0.0394657976 -0.0263461114 -0.1013346163 0.0986445415
[66] 0.0613074252 -0.0146985962 0.0140252454 -0.0900866813 -0.0560704356
[71] -0.0539728132 0.0482624005 0.0308631787 0.0954213982 -0.0489180408
[76] 0.0240471513 -0.0395869191 0.0548935842 -0.0247216731 -0.0089749646
[81] 0.0409593592 -0.0247216731 0.0243882326 -0.0361925511 0.0240471513
[86] -0.0878012048 0.0190767934 -0.0035064574 0.0095154156 -0.0718513291
[91] 0.0108323407 0.0108323407 0.0061524144 -0.0375820310 0.0783546864
[96] 0.0758901198 -0.0017394829 0.0609284988 -0.0131141808 -0.0017394829
[101] 0.0452778988 -0.0188890000 -0.0531294881 -0.0149786469 -0.0856836006
[106] -0.0108543417 0.0613074252 -0.0246014493 0.0292874396 0.0496987952
[111] 0.0733137830 0.0677795031 -0.0539728132 0.0292874396 0.0086189206
[116] -0.0765785938 0.0818557266 0.0191649555 -0.0510104831 -0.0053012048
[121] 0.0867139959 -0.0089749646 0.0409593592 -0.0265610438 -0.0035064574
[126] -0.0027433479 -0.0424279105 0.0276833414 0.0000000000 0.1523107355
[131] -0.0436781609 0.0703239519 0.0009001153 -0.0468523724 0.0348153376
[136] 0.0256192450 0.0256192450 -0.0035064574 0.0271644333 -0.0341683778
[141] -0.0108543417 0.0298992890 -0.0560704356 0.0703239519 -0.0721366479
[146] -0.0369278973 -0.0457642516 0.0240471513 -0.0053012048 -0.0375820310
[151] -0.0428018076 -0.0027433479 -0.0609528487 0.0108323407 0.0276833414
[156] 0.0529610014 -0.0302023558 0.0467980296 -0.0089749646 -0.0833042596
[161] -0.0168710805 0.0339315128 0.0379442982 0.0009001153 0.0315683056
[166] 0.0308631787 0.0157677185 0.0453050786 0.0771359700 0.0026790108
[171] 0.0394657976 0.0108323407 0.0544231807 -0.0436781609 0.0111564042
[176] 0.0158613373 0.0125366330 0.0482624005 -0.0468523724 0.0409593592
[181] 0.0026790108 -0.0547273841 0.0174825175 0.0292874396 -0.0428018076
[186] -0.0282605410 0.0276833414 -0.0603448276 0.0529610014 -0.0225988701
[191] -0.0521809270 -0.0361925511 -0.0285484057 -0.0560704356 -0.0207655142
[196] -0.0457642516 0.0276833414 -0.0071239718 -0.0382440232 -0.0408169680
[201] 0.0044296788 0.0240471513 0.0453050786 -0.0265610438 0.0073381465
[206] -0.0766935895 -0.0609528487 0.0771359700 0.0174808406 0.0363943215
[211] -0.0403225806 -0.0489180408 0.0240471513 0.0840677966 -0.0134232320
[216] -0.0027433479 -0.0743450390 0.0243882326 0.0900813854 -0.0302023558
[221] -0.0361925511 -0.0552747525 0.0061524144 0.0758901198 -0.0149786469
[226] -0.0089749646 -0.0721366479 -0.0108543417 -0.0367726584 0.0066895572
[231] 0.1065699007 0.0226963618 0.0208204399 -0.0053012048 0.1403770767
[236] -0.0149786469 0.0409593592 0.0637566081 0.0986445415 0.0033977556
[241] -0.0302023558 0.0911537350 0.0191649555 0.0758901198 -0.0321716293
[246] -0.0510104831 0.0224476969 -0.0375820310 0.0142128408 -0.0356043522
[251] -0.0341683778 -0.0539728132 0.0018787251 -0.0966453136 0.0090996169
[256] -0.0187915885 0.0026790108 -0.0498575499 -0.0187915885 0.0260504202
[261] -0.0702179177 0.0942928040 -0.0531294881 -0.0436781609 -0.0265610438
[266] 0.0703239519 -0.0071239718 -0.0375820310 0.0271644333 0.0037279048
[271] 0.0438648590 0.0224476969 -0.0674151311 0.0009001153 -0.0788367979
[276] 0.0482624005 -0.0531294881 0.1403770767 -0.0356043522 0.0373909332
[281] -0.0246014493 0.0090996169 0.0142128408 -0.0510104831 0.0613074252
[286] -0.0046082949 0.0878623188 0.0467980296 0.0174825175 -0.0765785938
[291] 0.0018787251 0.0348153376 0.0409593592 -0.0059322034 0.0292874396
[296] -0.0009072658 -0.0089749646 0.0276833414 0.0795470497 -0.0510104831
[301] 0.0715570836 -0.0071239718 0.0394657976 0.0613074252 -0.0603448276
[306] -0.0131141808 -0.0246014493 -0.0302023558 -0.0071239718 0.0348153376
[311] 0.0558560192 -0.0356043522 -0.0317304241 0.0108323407 -0.0166634744
[316] 0.0637566081 -0.0112775240 -0.0656660413 0.0482624005 0.0379442982
[321] 0.0037279048 0.0226963618 -0.0457642516 -0.0187915885 -0.0669490854
[326] -0.0263461114 0.0260504202 -0.0408169680 -0.0027433479 0.0379442982
[331] 0.0437829470 0.0208204399 -0.0625210084 0.0108323407 -0.0076867914
[336] -0.0489180408 -0.0382440232 0.0409593592 0.0157677185 -0.1109688519
[341] -0.0227169468 -0.0168710805 -0.0149786469 -0.0265610438 0.0044296788
[346] -0.0285484057 -0.0112775240 -0.0302023558 0.0026790108 -0.0834244649
[351] 0.0140252454 0.0363943215 -0.0168710805 -0.0468523724 -0.0046082949
[356] -0.0467170478 -0.0603448276 0.0276833414 -0.0149786469 0.0108323407
[361] 0.0332068311 0.0332068311 0.0061524144 -0.0428018076 0.0383336530
[366] 0.0226963618 -0.0207655142 -0.0027433479 -0.1265233623 0.0157677185
[371] 0.0090996169 0.0308631787 -0.0652350571 -0.0053012048 -0.0436781609
[376] 0.0157677185 -0.0448136082 0.0174825175 -0.0989785044 -0.0539728132
[381] 0.0529610014 0.0276833414 -0.0089749646 0.1396910248 0.0208204399
[386] 0.0000000000 -0.0131141808 0.0140252454 -0.0630808697 0.0783546864
[391] -0.0521809270 -0.0285484057 -0.0166634744 0.0026790108 -0.0718513291
[396] -0.0263461114 0.0256192450 -0.0321716293 0.0044296788 0.0055476529
[401] -0.0674151311 0.0690649924 0.0422310413 0.0677795031 0.0090996169
[406] -0.0166634744 -0.0187915885 0.0558560192 -0.0574458683 0.0190767934
[411] 0.0379442982 -0.0356043522 -0.0970839260 0.0240471513 0.0467980296
[416] -0.1030789826 -0.0168710805 0.0453050786 0.0524900713 -0.0321716293
[421] 0.0878623188 -0.0112775240 -0.0478400296 -0.0094684743 -0.0071239718
[426] 0.0271644333 -0.0428018076 0.0409593592 0.0572601936 -0.0855402456
[431] -0.0560704356 -0.0718513291 0.0394657976 -0.0321716293 0.0260504202
[436] -0.0652350571 0.0271644333 -0.0009072658 -0.0168710805 -0.0094684743
[441] -0.0112775240 -0.0265610438 0.0437829470 -0.0321716293 0.0453050786
[446] 0.0739485883 -0.0046082949 0.0467980296 -0.0336538462 0.0044296788
[451] -0.0468523724 -0.0321716293 0.0018787251 0.0511078180 -0.0035064574
[456] -0.0721366479 0.0224476969 -0.0395869191 0.0224476969 0.0243882326
[461] -0.0246014493 -0.0035064574 0.0453050786 -0.0084251317 -0.0416189931
[466] 0.0424255297 -0.0302023558 -0.0457642516 -0.0302023558 0.0308631787
[471] 0.0394657976 -0.0017394829 -0.0674151311 -0.0089749646 0.0315683056
[476] -0.0094684743 0.0260504202 0.0108323407 0.0931354698 0.0095154156
[481] 0.0324110390 0.0044296788 -0.0468523724 0.0073381465 -0.0531294881
[486] -0.0207655142 0.0174808406 0.0292874396 -0.0346758968 -0.0207402180
[491] 0.0026790108 -0.0089749646 -0.0552747525 -0.0539728132 -0.0603448276
[496] 0.0586363766 0.0174808406 0.0599852344 0.0073381465 -0.0382440232
$pvalue
[1] 0.63
$expectation
[1] 0.3179348
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