BonEV-package: BonEV: An Improved Multiple Testing Procedure for Controlling...
In BonEV: An Improved Multiple Testing Procedure for Controlling False Discovery Rates
Description
Details
Author(s)
See Also
Examples
Description
BonEV is an improved multiple testing procedure for controlling false discovery rates which is developed based on the Bonferroni procedure with integrated estimates from the Benjamini-Hochberg procedure and the Storey's q-value procedure. It controls false discovery rates through controlling the expected number of false discoveries.
Details
Package: BonEV
Type: Package
Version: 1.0.0
Date: 2015-02-10
Depends: R (>= 3.2.0), qvalue
License: GPL (>= 2)
Author(s)
Dongmei Li
Maintainer: Dongmei Li <dongmei_li@urmc.rochester.edu>
See Also
The Bon_EV function defined in this package.
The qvalue package.
Examples
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library(qvalue)
data(hedenfalk)
summary(hedenfalk)
pvalues <- hedenfalk$p
adjp <- Bon_EV(pvalues, 0.05)
summary(adjp)
results <- cbind(adjp$raw_P_value, adjp$BH_adjp, adjp$Storey_adjp, adjp$Bon_EV_adjp)
results
##Compare with Benjamini-Hochberg and Storey's q-value procedures
sum(adjp$raw_P_value <= 0.05)
sum(adjp$BH_adjp <= 0.05)
sum(adjp$Storey_adjp <= 0.05)
sum(adjp$Bon_EV_adjp <= 0.05)
Example output
Loading required package: qvalue
Length Class Mode
p 3170 -none- numeric
stat 3170 -none- numeric
stat0 317000 -none- numeric
Length Class Mode
raw_P_value 3170 -none- numeric
BH_adjp 3170 -none- numeric
Storey_adjp 3170 -none- numeric
Bon_EV_adjp 3170 -none- numeric
[,1] [,2] [,3] [,4]
[1,] 1.212618e-02 0.13164384 0.08819163 2.739570e-01
[2,] 7.502524e-02 0.31252300 0.20936729 1.000000e+00
[3,] 9.949211e-01 0.99712298 0.66799864 1.000000e+00
[4,] 4.178549e-02 0.24127505 0.16163643 9.440255e-01
[5,] 8.458139e-01 0.94409507 0.63247386 1.000000e+00
[6,] 2.519243e-01 0.55487215 0.37172329 1.000000e+00
[7,] 6.586562e-01 0.85571311 0.57326449 1.000000e+00
[8,] 6.568139e-02 0.29288112 0.19620868 1.000000e+00
[9,] 1.232681e-01 0.40326109 0.27015510 1.000000e+00
[10,] 7.129338e-04 0.03455882 0.02315186 1.610673e-02
[11,] 8.839748e-02 0.34467564 0.23090718 1.000000e+00
[12,] 7.381703e-03 0.10263158 0.06875557 1.667688e-01
[13,] 2.710000e-01 0.56872932 0.38100657 1.000000e+00
[14,] 9.749811e-01 0.99124118 0.66405827 1.000000e+00
[15,] 2.497098e-01 0.55277933 0.37032126 1.000000e+00
[16,] 7.734763e-01 0.91832210 0.61520787 1.000000e+00
[17,] 3.618297e-02 0.22569472 0.15119876 8.174523e-01
[18,] 1.750789e-03 0.05441176 0.03645186 3.955414e-02
[19,] 8.846688e-02 0.34467564 0.23090718 1.000000e+00
[20,] 1.380883e-01 0.42947059 0.28771352 1.000000e+00
[21,] 8.469748e-01 0.94505808 0.63311900 1.000000e+00
[22,] 3.630410e-01 0.65649743 0.43980472 1.000000e+00
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[27,] 3.367886e-01 0.63165582 0.42316268 1.000000e+00
[28,] 6.235079e-01 0.83679932 0.56059365 1.000000e+00
[29,] 2.649842e-03 0.06407407 0.04292489 5.986573e-02
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[58,] 4.046057e-02 0.23973832 0.16060694 9.140927e-01
[59,] 4.200473e-01 0.69874082 0.46810466 1.000000e+00
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[64,] 7.937098e-01 0.92617045 0.62046569 1.000000e+00
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[166,] 9.899748e-01 0.99654430 0.66761097 1.000000e+00
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[168,] 2.328360e-01 0.53601307 0.35908911 1.000000e+00
[169,] 1.403785e-02 0.14448052 0.09679126 3.171458e-01
[170,] 2.698580e-01 0.56802789 0.38053667 1.000000e+00
[171,] 3.746435e-01 0.66384572 0.44472753 1.000000e+00
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[221,] 1.549905e-01 0.45230487 0.30301080 1.000000e+00
[222,] 4.310347e-01 0.70760228 0.47404118 1.000000e+00
[223,] 4.133691e-01 0.69500000 0.46559859 1.000000e+00
[224,] 6.669306e-01 0.86116904 0.57691955 1.000000e+00
[225,] 1.400694e-01 0.43276803 0.28992257 1.000000e+00
[226,] 1.244479e-02 0.13418367 0.08989314 2.811551e-01
[227,] 1.291199e-01 0.41512170 0.27810083 1.000000e+00
[228,] 2.374637e-01 0.54239741 0.36336614 1.000000e+00
[229,] 3.160032e-01 0.61380515 0.41120404 1.000000e+00
[230,] 3.340662e-01 0.62885392 0.42128561 1.000000e+00
[231,] 1.895584e-02 0.16691667 0.11182182 4.282538e-01
[232,] 1.101987e-01 0.38568282 0.25837896 1.000000e+00
[233,] 4.268265e-01 0.70324324 0.47112095 1.000000e+00
[234,] 2.036530e-01 0.51159684 0.34273204 1.000000e+00
[235,] 5.639401e-01 0.79771977 0.53441323 1.000000e+00
[236,] 9.924164e-01 0.99654430 0.66761097 1.000000e+00
[237,] 2.670915e-01 0.56413724 0.37793022 1.000000e+00
[238,] 9.675394e-02 0.35872515 0.24031931 1.000000e+00
[239,] 2.126088e-01 0.52019985 0.34849542 1.000000e+00
[240,] 2.254132e-01 0.53039172 0.35532322 1.000000e+00
[241,] 2.291924e-01 0.53150585 0.35606960 1.000000e+00
[242,] 2.222397e-01 0.52892804 0.35434266 1.000000e+00
[243,] 3.937855e-02 0.23777143 0.15928927 8.896475e-01
[244,] 5.259590e-01 0.76983856 0.51573489 1.000000e+00
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[1906,] 4.858044e-03 0.08772727 0.05877078 1.097538e-01
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[1911,] 2.339369e-01 0.53803481 0.36044352 1.000000e+00
[1912,] 2.132303e-01 0.52019985 0.34849542 1.000000e+00
[1913,] 3.028833e-01 0.60132749 0.40284494 1.000000e+00
[1914,] 1.265363e-01 0.41014315 0.27476557 1.000000e+00
[1915,] 7.483249e-01 0.90645395 0.60725710 1.000000e+00
[1916,] 6.943312e-01 0.88076431 0.59004693 1.000000e+00
[1917,] 8.891009e-01 0.95898265 0.64244743 1.000000e+00
[1918,] 6.794953e-03 0.09880734 0.06619361 1.535128e-01
[1919,] 2.129054e-01 0.52019985 0.34849542 1.000000e+00
[1920,] 2.243975e-01 0.53039172 0.35532322 1.000000e+00
[1921,] 7.765300e-02 0.32031169 0.21458514 1.000000e+00
[1922,] 7.311672e-02 0.30945260 0.20731035 1.000000e+00
[1923,] 1.665521e-01 0.46755084 0.31322448 1.000000e+00
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[1925,] 4.363060e-01 0.71183222 0.47687493 1.000000e+00
[1926,] 6.973880e-01 0.88393443 0.59217068 1.000000e+00
[1927,] 4.018139e-01 0.68731536 0.46045045 1.000000e+00
[1928,] 4.167571e-01 0.69668595 0.46672805 1.000000e+00
[1929,] 6.359117e-01 0.84526205 0.56626305 1.000000e+00
[1930,] 7.000726e-01 0.88627396 0.59373799 1.000000e+00
[1931,] 2.520410e-01 0.55487215 0.37172329 1.000000e+00
[1932,] 2.996845e-04 0.03276596 0.02195077 6.770529e-03
[1933,] 7.238801e-02 0.30760054 0.20606960 1.000000e+00
[1934,] 1.911640e-01 0.49957955 0.33468135 1.000000e+00
[1935,] 2.594637e-02 0.19039352 0.12754957 5.861853e-01
[1936,] 3.408202e-02 0.22018219 0.14750578 7.699873e-01
[1937,] 9.016404e-01 0.96145931 0.64410662 1.000000e+00
[1938,] 4.798202e-01 0.74160410 0.49681988 1.000000e+00
[1939,] 8.254826e-01 0.93623614 0.62720895 1.000000e+00
[1940,] 6.410095e-03 0.09654028 0.06467485 1.448181e-01
[1941,] 7.659842e-01 0.91529190 0.61317787 1.000000e+00
[1942,] 2.371924e-02 0.18250000 0.12226150 5.358696e-01
[1943,] 1.667098e-01 0.46755084 0.31322448 1.000000e+00
[1944,] 1.590536e-02 0.15513846 0.10393129 3.593369e-01
[1945,] 1.069811e-01 0.38061728 0.25498542 1.000000e+00
[1946,] 2.579180e-01 0.55694823 0.37311411 1.000000e+00
[1947,] 2.893659e-01 0.58571155 0.39238341 1.000000e+00
[1948,] 1.424196e-01 0.43466795 0.29119537 1.000000e+00
[1949,] 9.529274e-01 0.98399414 0.65920328 1.000000e+00
[1950,] 5.303028e-01 0.77396869 0.51850177 1.000000e+00
[1951,] 2.168328e-01 0.52350343 0.35070857 1.000000e+00
[1952,] 2.621577e-01 0.55962290 0.37490594 1.000000e+00
[1953,] 3.350473e-01 0.62994076 0.42201371 1.000000e+00
[1954,] 6.255521e-02 0.28692197 0.19221649 1.000000e+00
[1955,] 6.229022e-02 0.28617391 0.19171535 1.000000e+00
[1956,] 2.248644e-01 0.53039172 0.35532322 1.000000e+00
[1957,] 7.256183e-01 0.89537174 0.59983283 1.000000e+00
[1958,] 8.533754e-02 0.33921151 0.22724662 1.000000e+00
[1959,] 4.042366e-01 0.68894086 0.46153941 1.000000e+00
[1960,] 4.961956e-01 0.75260287 0.50418825 1.000000e+00
[1961,] 1.999905e-01 0.50636581 0.33922764 1.000000e+00
[1962,] 7.255521e-05 0.01882353 0.01261037 1.639181e-03
[1963,] 2.417918e-01 0.54398017 0.36442647 1.000000e+00
[1964,] 6.296246e-01 0.84006313 0.56278016 1.000000e+00
[1965,] 8.557161e-01 0.94681326 0.63429485 1.000000e+00
[1966,] 4.627161e-01 0.72758433 0.48742768 1.000000e+00
[1967,] 5.713344e-01 0.80387483 0.53853667 1.000000e+00
[1968,] 8.326719e-01 0.93833037 0.62861194 1.000000e+00
[1969,] 9.361798e-01 0.98020806 0.65666689 1.000000e+00
[1970,] 5.002492e-01 0.75498099 0.50578141 1.000000e+00
[1971,] 9.247382e-01 0.97393023 0.65246121 1.000000e+00
[1972,] 4.516120e-01 0.71929719 0.48187591 1.000000e+00
[1973,] 8.237666e-01 0.93524884 0.62654754 1.000000e+00
[1974,] 5.808360e-01 0.81112335 0.54339264 1.000000e+00
[1975,] 1.325584e-01 0.42105210 0.28207376 1.000000e+00
[1976,] 5.533091e-01 0.79366063 0.53169391 1.000000e+00
[1977,] 7.155836e-01 0.89416994 0.59902772 1.000000e+00
[1978,] 9.397855e-01 0.98140270 0.65746721 1.000000e+00
[1979,] 1.476940e-01 0.44252363 0.29645810 1.000000e+00
[1980,] 8.004921e-01 0.92692868 0.62097364 1.000000e+00
[1981,] 5.615142e-04 0.03455882 0.02315186 1.268583e-02
[1982,] 2.959874e-01 0.59529785 0.39880552 1.000000e+00
[1983,] 6.649590e-01 0.86028968 0.57633045 1.000000e+00
[1984,] 5.302082e-01 0.77396869 0.51850177 1.000000e+00
[1985,] 6.827129e-02 0.29800550 0.19964164 1.000000e+00
[1986,] 4.763975e-01 0.73877751 0.49492628 1.000000e+00
[1987,] 1.597413e-01 0.45678990 0.30601544 1.000000e+00
[1988,] 3.069306e-01 0.60395407 0.40460455 1.000000e+00
[1989,] 7.948044e-01 0.92617045 0.62046569 1.000000e+00
[1990,] 4.470032e-03 0.08321637 0.05574881 1.009878e-01
[1991,] 3.266972e-01 0.62125375 0.41619406 1.000000e+00
[1992,] 2.979685e-01 0.59744466 0.40024372 1.000000e+00
[1993,] 1.767445e-01 0.48021404 0.32170788 1.000000e+00
[1994,] 8.755205e-01 0.95565382 0.64021737 1.000000e+00
[1995,] 8.743281e-01 0.95565382 0.64021737 1.000000e+00
[1996,] 7.030789e-01 0.88901476 0.59557412 1.000000e+00
[1997,] 5.974164e-01 0.82268028 0.55113493 1.000000e+00
[1998,] 9.733943e-01 0.99107223 0.66394508 1.000000e+00
[1999,] 8.862744e-01 0.95723680 0.64127784 1.000000e+00
[2000,] 8.267634e-01 0.93642169 0.62733326 1.000000e+00
[2001,] 6.501356e-01 0.85127220 0.57028940 1.000000e+00
[2002,] 9.695962e-01 0.99107223 0.66394508 1.000000e+00
[2003,] 4.439748e-01 0.71623410 0.47982386 1.000000e+00
[2004,] 8.604795e-01 0.95075636 0.63693643 1.000000e+00
[2005,] 7.677256e-01 0.91597818 0.61363762 1.000000e+00
[2006,] 4.576151e-01 0.72423365 0.48518297 1.000000e+00
[2007,] 1.411230e-01 0.43377176 0.29059499 1.000000e+00
[2008,] 5.194006e-02 0.26673667 0.17869384 1.000000e+00
[2009,] 2.669180e-01 0.56413724 0.37793022 1.000000e+00
[2010,] 9.528013e-01 0.98399414 0.65920328 1.000000e+00
[2011,] 1.467319e-01 0.44130930 0.29564458 1.000000e+00
[2012,] 7.263785e-01 0.89553225 0.59994036 1.000000e+00
[2013,] 9.926183e-01 0.99654430 0.66761097 1.000000e+00
[2014,] 8.684227e-01 0.95309713 0.63850457 1.000000e+00
[2015,] 7.732492e-01 0.91832210 0.61520787 1.000000e+00
[2016,] 7.101830e-01 0.89085443 0.59680657 1.000000e+00
[2017,] 9.540757e-01 0.98416721 0.65931923 1.000000e+00
[2018,] 1.671009e-01 0.46756399 0.31323329 1.000000e+00
[2019,] 2.270126e-01 0.53109225 0.35579252 1.000000e+00
[2020,] 8.240221e-01 0.93524884 0.62654754 1.000000e+00
[2021,] 2.910631e-01 0.58694020 0.39320652 1.000000e+00
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[2023,] 2.910410e-02 0.20108932 0.13471497 6.575253e-01
[2024,] 8.904385e-01 0.95977219 0.64297637 1.000000e+00
[2025,] 3.376309e-01 0.63181228 0.42326749 1.000000e+00
[2026,] 7.617382e-01 0.91415437 0.61241580 1.000000e+00
[2027,] 4.794953e-04 0.03276596 0.02195077 1.083285e-02
[2028,] 3.812050e-01 0.67016602 0.44896166 1.000000e+00
[2029,] 4.959306e-02 0.26044702 0.17448024 1.000000e+00
[2030,] 2.563091e-02 0.18895349 0.12658486 5.790584e-01
[2031,] 7.640252e-01 0.91499622 0.61297978 1.000000e+00
[2032,] 6.732334e-01 0.86472853 0.57930414 1.000000e+00
[2033,] 4.315457e-03 0.08240964 0.05520836 9.749562e-02
[2034,] 5.554196e-01 0.79462128 0.53233748 1.000000e+00
[2035,] 4.422902e-01 0.71623218 0.47982258 1.000000e+00
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[2040,] 7.014543e-01 0.88766866 0.59467234 1.000000e+00
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[3074,] 9.516435e-01 0.98399414 0.65920328 1.000000e+00
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[3076,] 3.235016e-02 0.21392931 0.14331682 7.308608e-01
[3077,] 2.216845e-01 0.52846617 0.35403324 1.000000e+00
[3078,] 7.960315e-01 0.92617045 0.62046569 1.000000e+00
[3079,] 9.898107e-01 0.99654430 0.66761097 1.000000e+00
[3080,] 8.203975e-01 0.93519914 0.62651424 1.000000e+00
[3081,] 9.077918e-02 0.35008516 0.23453116 1.000000e+00
[3082,] 1.027981e-01 0.37072810 0.24836040 1.000000e+00
[3083,] 1.729338e-02 0.16040816 0.10746160 3.906952e-01
[3084,] 1.054259e-01 0.37717024 0.25267616 1.000000e+00
[3085,] 1.836025e-01 0.48794486 0.32688696 1.000000e+00
[3086,] 4.087382e-01 0.69214744 0.46368758 1.000000e+00
[3087,] 6.232114e-01 0.83675561 0.56056436 1.000000e+00
[3088,] 2.848454e-01 0.58068167 0.38901377 1.000000e+00
[3089,] 2.094511e-01 0.51790952 0.34696106 1.000000e+00
[3090,] 1.542587e-01 0.45230487 0.30301080 1.000000e+00
[3091,] 7.643249e-01 0.91499622 0.61297978 1.000000e+00
[3092,] 9.617035e-01 0.98884204 0.66245102 1.000000e+00
[3093,] 6.493281e-01 0.85097107 0.57008767 1.000000e+00
[3094,] 3.081420e-01 0.60483591 0.40519532 1.000000e+00
[3095,] 8.211640e-01 0.93519914 0.62651424 1.000000e+00
[3096,] 6.119243e-01 0.82937260 0.55561829 1.000000e+00
[3097,] 8.649842e-02 0.34075776 0.22828249 1.000000e+00
[3098,] 6.712934e-03 0.09851852 0.06600012 1.516598e-01
[3099,] 4.100946e-04 0.03276596 0.02195077 9.264934e-03
[3100,] 9.437571e-01 0.98241153 0.65814305 1.000000e+00
[3101,] 6.495710e-01 0.85097107 0.57008767 1.000000e+00
[3102,] 8.952334e-01 0.96044504 0.64342713 1.000000e+00
[3103,] 2.760379e-01 0.57404590 0.38456829 1.000000e+00
[3104,] 1.972618e-01 0.50266881 0.33675092 1.000000e+00
[3105,] 1.583817e-01 0.45650995 0.30582789 1.000000e+00
[3106,] 8.957256e-01 0.96044504 0.64342713 1.000000e+00
[3107,] 9.247729e-01 0.97393023 0.65246121 1.000000e+00
[3108,] 4.456909e-01 0.71728057 0.48052492 1.000000e+00
[3109,] 6.076814e-01 0.82937260 0.55561829 1.000000e+00
[3110,] 8.498801e-01 0.94681326 0.63429485 1.000000e+00
[3111,] 2.729369e-01 0.57071900 0.38233951 1.000000e+00
[3112,] 2.015773e-02 0.17229111 0.11542230 4.554072e-01
[3113,] 9.550284e-01 0.98453333 0.65956450 1.000000e+00
[3114,] 3.861956e-01 0.67451240 0.45187341 1.000000e+00
[3115,] 9.512776e-01 0.98399414 0.65920328 1.000000e+00
[3116,] 2.905615e-01 0.58653724 0.39293656 1.000000e+00
[3117,] 1.279401e-01 0.41311609 0.27675722 1.000000e+00
[3118,] 6.511041e-02 0.29276204 0.19612891 1.000000e+00
[3119,] 3.213533e-01 0.61664044 0.41310348 1.000000e+00
[3120,] 2.787792e-01 0.57497072 0.38518785 1.000000e+00
[3121,] 5.255457e-01 0.76983856 0.51573489 1.000000e+00
[3122,] 2.026372e-01 0.51093800 0.34229066 1.000000e+00
[3123,] 3.947950e-01 0.68127382 0.45640306 1.000000e+00
[3124,] 3.563249e-01 0.65040276 0.43572174 1.000000e+00
[3125,] 6.471735e-01 0.85097107 0.57008767 1.000000e+00
[3126,] 7.114826e-02 0.30355316 0.20335816 1.000000e+00
[3127,] 4.812366e-01 0.74279942 0.49762066 1.000000e+00
[3128,] 1.892429e-02 0.16691667 0.11182182 4.275411e-01
[3129,] 5.788644e-03 0.09295000 0.06226962 1.307781e-01
[3130,] 8.439432e-02 0.33786885 0.22634714 1.000000e+00
[3131,] 1.200063e-01 0.39918153 0.26742210 1.000000e+00
[3132,] 8.711640e-01 0.95359116 0.63883554 1.000000e+00
[3133,] 4.334921e-01 0.71053257 0.47600426 1.000000e+00
[3134,] 3.928391e-02 0.23765267 0.15920971 8.875094e-01
[3135,] 4.260536e-01 0.70270031 0.47075723 1.000000e+00
[3136,] 4.441325e-02 0.24786972 0.16605438 1.000000e+00
[3137,] 2.558833e-01 0.55644277 0.37277549 1.000000e+00
[3138,] 3.488013e-02 0.22177645 0.14857381 7.880183e-01
[3139,] 9.992681e-01 0.99985174 0.66982670 1.000000e+00
[3140,] 3.210347e-01 0.61640218 0.41294386 1.000000e+00
[3141,] 4.097792e-02 0.24053407 0.16114003 9.257808e-01
[3142,] 8.219180e-01 0.93519914 0.62651424 1.000000e+00
[3143,] 8.315142e-02 0.33578344 0.22495007 1.000000e+00
[3144,] 7.664606e-01 0.91529190 0.61317787 1.000000e+00
[3145,] 2.434069e-02 0.18415274 0.12336872 5.499095e-01
[3146,] 1.837129e-01 0.48794486 0.32688696 1.000000e+00
[3147,] 4.554826e-01 0.72338677 0.48461563 1.000000e+00
[3148,] 4.910726e-02 0.26021703 0.17432616 1.000000e+00
[3149,] 7.251987e-01 0.89537174 0.59983283 1.000000e+00
[3150,] 2.551735e-02 0.18855478 0.12631775 5.764927e-01
[3151,] 4.500915e-01 0.71929613 0.48187520 1.000000e+00
[3152,] 6.112366e-01 0.82937260 0.55561829 1.000000e+00
[3153,] 6.381703e-03 0.09654028 0.06467485 1.441766e-01
[3154,] 6.195899e-02 0.28617391 0.19171535 1.000000e+00
[3155,] 9.425836e-01 0.98224523 0.65803165 1.000000e+00
[3156,] 9.615773e-02 0.35708431 0.23922007 1.000000e+00
[3157,] 1.782019e-02 0.16279539 0.10906087 4.025970e-01
[3158,] 5.142681e-01 0.76393158 0.51177765 1.000000e+00
[3159,] 2.749211e-02 0.19773756 0.13246954 6.211069e-01
[3160,] 5.579180e-01 0.79621294 0.53340377 1.000000e+00
[3161,] 9.495268e-03 0.11567050 0.07749068 2.145189e-01
[3162,] 6.098423e-01 0.82937260 0.55561829 1.000000e+00
[3163,] 5.788644e-03 0.09295000 0.06226962 1.307781e-01
[3164,] 1.227950e-01 0.40324017 0.27014108 1.000000e+00
[3165,] 4.115457e-02 0.24053407 0.16114003 9.297718e-01
[3166,] 5.249211e-02 0.26709470 0.17893369 1.000000e+00
[3167,] 3.374132e-01 0.63181228 0.42326749 1.000000e+00
[3168,] 5.399716e-01 0.78171689 0.52369249 1.000000e+00
[3169,] 2.546751e-01 0.55562285 0.37222621 1.000000e+00
[3170,] 1.792114e-02 0.16324713 0.10936350 4.048776e-01
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BonEV documentation built on May 2, 2019, 8:51 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Details Author(s) See Also Examples
Description
BonEV is an improved multiple testing procedure for controlling false discovery rates which is developed based on the Bonferroni procedure with integrated estimates from the Benjamini-Hochberg procedure and the Storey's q-value procedure. It controls false discovery rates through controlling the expected number of false discoveries.
Details
| Package: | BonEV |
| Type: | Package |
| Version: | 1.0.0 |
| Date: | 2015-02-10 |
| Depends: | R (>= 3.2.0), qvalue |
| License: | GPL (>= 2) |
Author(s)
Dongmei Li Maintainer: Dongmei Li <dongmei_li@urmc.rochester.edu>
See Also
The Bon_EV function defined in this package.
The qvalue package.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | library(qvalue)
data(hedenfalk)
summary(hedenfalk)
pvalues <- hedenfalk$p
adjp <- Bon_EV(pvalues, 0.05)
summary(adjp)
results <- cbind(adjp$raw_P_value, adjp$BH_adjp, adjp$Storey_adjp, adjp$Bon_EV_adjp)
results
##Compare with Benjamini-Hochberg and Storey's q-value procedures
sum(adjp$raw_P_value <= 0.05)
sum(adjp$BH_adjp <= 0.05)
sum(adjp$Storey_adjp <= 0.05)
sum(adjp$Bon_EV_adjp <= 0.05)
|
Example output
Loading required package: qvalue
Length Class Mode
p 3170 -none- numeric
stat 3170 -none- numeric
stat0 317000 -none- numeric
Length Class Mode
raw_P_value 3170 -none- numeric
BH_adjp 3170 -none- numeric
Storey_adjp 3170 -none- numeric
Bon_EV_adjp 3170 -none- numeric
[,1] [,2] [,3] [,4]
[1,] 1.212618e-02 0.13164384 0.08819163 2.739570e-01
[2,] 7.502524e-02 0.31252300 0.20936729 1.000000e+00
[3,] 9.949211e-01 0.99712298 0.66799864 1.000000e+00
[4,] 4.178549e-02 0.24127505 0.16163643 9.440255e-01
[5,] 8.458139e-01 0.94409507 0.63247386 1.000000e+00
[6,] 2.519243e-01 0.55487215 0.37172329 1.000000e+00
[7,] 6.586562e-01 0.85571311 0.57326449 1.000000e+00
[8,] 6.568139e-02 0.29288112 0.19620868 1.000000e+00
[9,] 1.232681e-01 0.40326109 0.27015510 1.000000e+00
[10,] 7.129338e-04 0.03455882 0.02315186 1.610673e-02
[11,] 8.839748e-02 0.34467564 0.23090718 1.000000e+00
[12,] 7.381703e-03 0.10263158 0.06875557 1.667688e-01
[13,] 2.710000e-01 0.56872932 0.38100657 1.000000e+00
[14,] 9.749811e-01 0.99124118 0.66405827 1.000000e+00
[15,] 2.497098e-01 0.55277933 0.37032126 1.000000e+00
[16,] 7.734763e-01 0.91832210 0.61520787 1.000000e+00
[17,] 3.618297e-02 0.22569472 0.15119876 8.174523e-01
[18,] 1.750789e-03 0.05441176 0.03645186 3.955414e-02
[19,] 8.846688e-02 0.34467564 0.23090718 1.000000e+00
[20,] 1.380883e-01 0.42947059 0.28771352 1.000000e+00
[21,] 8.469748e-01 0.94505808 0.63311900 1.000000e+00
[22,] 3.630410e-01 0.65649743 0.43980472 1.000000e+00
[23,] 1.798738e-01 0.48363020 0.32399645 1.000000e+00
[24,] 9.964795e-01 0.99805371 0.66862216 1.000000e+00
[25,] 9.418580e-01 0.98181190 0.65774135 1.000000e+00
[26,] 5.461893e-01 0.78700909 0.52723787 1.000000e+00
[27,] 3.367886e-01 0.63165582 0.42316268 1.000000e+00
[28,] 6.235079e-01 0.83679932 0.56059365 1.000000e+00
[29,] 2.649842e-03 0.06407407 0.04292489 5.986573e-02
[30,] 6.738139e-01 0.86512353 0.57956877 1.000000e+00
[31,] 6.793123e-01 0.86936617 0.58241102 1.000000e+00
[32,] 1.167413e-01 0.39510616 0.26469190 1.000000e+00
[33,] 7.954574e-01 0.92617045 0.62046569 1.000000e+00
[34,] 8.524763e-01 0.94681326 0.63429485 1.000000e+00
[35,] 1.164038e-03 0.04500000 0.03014667 2.629816e-02
[36,] 5.741956e-01 0.80611160 0.54003514 1.000000e+00
[37,] 6.279180e-02 0.28710375 0.19233827 1.000000e+00
[38,] 4.164984e-02 0.24127505 0.16163643 9.409610e-01
[39,] 2.710883e-01 0.56872932 0.38100657 1.000000e+00
[40,] 4.470946e-01 0.71797872 0.48099263 1.000000e+00
[41,] 5.621672e-01 0.79656836 0.53364188 1.000000e+00
[42,] 8.167792e-01 0.93430736 0.62591682 1.000000e+00
[43,] 6.425868e-03 0.09654028 0.06467485 1.451744e-01
[44,] 2.806309e-02 0.19930649 0.13352060 6.340066e-01
[45,] 4.525868e-02 0.24870466 0.16661373 1.000000e+00
[46,] 1.701514e-01 0.47314035 0.31696904 1.000000e+00
[47,] 2.819874e-01 0.57782805 0.38710205 1.000000e+00
[48,] 5.393691e-02 0.27182830 0.18210485 1.000000e+00
[49,] 7.211199e-01 0.89537174 0.59983283 1.000000e+00
[50,] 2.026246e-01 0.51093800 0.34229066 1.000000e+00
[51,] 1.974606e-01 0.50277108 0.33681943 1.000000e+00
[52,] 2.346467e-01 0.53861694 0.36083351 1.000000e+00
[53,] 3.770095e-01 0.66691964 0.44678683 1.000000e+00
[54,] 8.111735e-01 0.93171129 0.62417764 1.000000e+00
[55,] 5.191262e-01 0.76647881 0.51348410 1.000000e+00
[56,] 2.831199e-01 0.57865248 0.38765436 1.000000e+00
[57,] 1.432650e-01 0.43668269 0.29254510 1.000000e+00
[58,] 4.046057e-02 0.23973832 0.16060694 9.140927e-01
[59,] 4.200473e-01 0.69874082 0.46810466 1.000000e+00
[60,] 2.984227e-03 0.06686667 0.04479572 6.742022e-02
[61,] 1.857476e-01 0.49109258 0.32899570 1.000000e+00
[62,] 4.265268e-01 0.70311492 0.47103499 1.000000e+00
[63,] 9.834890e-01 0.99383487 0.66579585 1.000000e+00
[64,] 7.937098e-01 0.92617045 0.62046569 1.000000e+00
[65,] 7.024984e-01 0.88863528 0.59531990 1.000000e+00
[66,] 5.437224e-01 0.78559708 0.52629193 1.000000e+00
[67,] 4.941041e-01 0.75122782 0.50326707 1.000000e+00
[68,] 8.438013e-01 0.94409507 0.63247386 1.000000e+00
[69,] 3.712429e-01 0.66114607 0.44291896 1.000000e+00
[70,] 5.087129e-01 0.75939351 0.50873748 1.000000e+00
[71,] 9.478139e-01 0.98292579 0.65848757 1.000000e+00
[72,] 4.952965e-01 0.75195881 0.50375678 1.000000e+00
[73,] 1.310726e-02 0.13896321 0.09309507 2.961216e-01
[74,] 4.095079e-01 0.69308062 0.46431275 1.000000e+00
[75,] 7.830095e-01 0.92438700 0.61927091 1.000000e+00
[76,] 1.347445e-01 0.42451837 0.28439591 1.000000e+00
[77,] 1.880536e-01 0.49389395 0.33087241 1.000000e+00
[78,] 7.705363e-01 0.91743619 0.61461438 1.000000e+00
[79,] 4.654574e-02 0.25192833 0.16877334 1.000000e+00
[80,] 2.005331e-01 0.50733440 0.33987652 1.000000e+00
[81,] 1.118517e-01 0.38793217 0.25988585 1.000000e+00
[82,] 8.750789e-03 0.11140000 0.07462976 1.976994e-01
[83,] 5.854574e-02 0.28119697 0.18838117 1.000000e+00
[84,] 1.824101e-01 0.48714406 0.32635048 1.000000e+00
[85,] 2.363281e-01 0.54090975 0.36236952 1.000000e+00
[86,] 4.249495e-01 0.70270031 0.47075723 1.000000e+00
[87,] 2.609968e-01 0.55962290 0.37490594 1.000000e+00
[88,] 1.709779e-02 0.15988201 0.10710912 3.862765e-01
[89,] 2.247950e-02 0.18009975 0.12065351 5.078609e-01
[90,] 6.696309e-01 0.86184734 0.57737396 1.000000e+00
[91,] 4.643249e-01 0.72902922 0.48839565 1.000000e+00
[92,] 1.230284e-02 0.13310580 0.08917104 2.779480e-01
[93,] 9.713975e-01 0.99107223 0.66394508 1.000000e+00
[94,] 4.255521e-03 0.08175758 0.05477153 9.614151e-02
[95,] 2.353312e-03 0.05920635 0.03966387 5.316647e-02
[96,] 7.210095e-02 0.30679195 0.20552791 1.000000e+00
[97,] 9.495174e-01 0.98332898 0.65875767 1.000000e+00
[98,] 8.358675e-02 0.33669632 0.22556162 1.000000e+00
[99,] 2.011609e-01 0.50851675 0.34066860 1.000000e+00
[100,] 5.499937e-01 0.79033545 0.52946629 1.000000e+00
[101,] 3.565205e-01 0.65040276 0.43572174 1.000000e+00
[102,] 5.039621e-01 0.75785579 0.50770732 1.000000e+00
[103,] 1.078549e-01 0.38185268 0.25581305 1.000000e+00
[104,] 5.456593e-01 0.78688495 0.52715471 1.000000e+00
[105,] 3.063817e-01 0.60329193 0.40416096 1.000000e+00
[106,] 6.381230e-01 0.84673504 0.56724984 1.000000e+00
[107,] 5.950410e-01 0.82077391 0.54985781 1.000000e+00
[108,] 7.170284e-01 0.89416994 0.59902772 1.000000e+00
[109,] 9.567729e-01 0.98517701 0.65999572 1.000000e+00
[110,] 4.100946e-04 0.03276596 0.02195077 9.264934e-03
[111,] 1.444164e-02 0.14761146 0.09888876 3.262682e-01
[112,] 7.233754e-01 0.89537174 0.59983283 1.000000e+00
[113,] 4.808013e-01 0.74275828 0.49759311 1.000000e+00
[114,] 1.339117e-02 0.14102990 0.09447960 3.025357e-01
[115,] 6.682934e-01 0.86120325 0.57694247 1.000000e+00
[116,] 7.327350e-01 0.89873114 0.60208338 1.000000e+00
[117,] 6.593060e-04 0.03455882 0.02315186 1.489516e-02
[118,] 4.862397e-01 0.74570876 0.49956970 1.000000e+00
[119,] 7.815804e-01 0.92413652 0.61910310 1.000000e+00
[120,] 8.185426e-01 0.93505586 0.62641825 1.000000e+00
[121,] 2.150662e-01 0.52122324 0.34918102 1.000000e+00
[122,] 4.122681e-01 0.69441552 0.46520703 1.000000e+00
[123,] 5.892461e-01 0.81616863 0.54677261 1.000000e+00
[124,] 4.975521e-01 0.75306006 0.50449453 1.000000e+00
[125,] 5.645741e-02 0.28095761 0.18822082 1.000000e+00
[126,] 1.580442e-02 0.15462963 0.10359041 3.570563e-01
[127,] 4.587413e-01 0.72440299 0.48529641 1.000000e+00
[128,] 5.183849e-01 0.76609790 0.51322892 1.000000e+00
[129,] 8.530978e-01 0.94681326 0.63429485 1.000000e+00
[130,] 2.227129e-03 0.05803279 0.03887767 5.031572e-02
[131,] 1.901893e-02 0.16700831 0.11188321 4.296792e-01
[132,] 9.648076e-01 0.99042381 0.66351069 1.000000e+00
[133,] 1.736562e-01 0.47712435 0.31963802 1.000000e+00
[134,] 3.793028e-01 0.66933333 0.44840382 1.000000e+00
[135,] 7.179180e-02 0.30588710 0.20492173 1.000000e+00
[136,] 9.394322e-02 0.35448276 0.23747723 1.000000e+00
[137,] 4.557760e-01 0.72349024 0.48468494 1.000000e+00
[138,] 5.205678e-01 0.76789204 0.51443087 1.000000e+00
[139,] 3.429022e-03 0.06955414 0.04659613 7.746911e-02
[140,] 2.893659e-01 0.58571155 0.39238341 1.000000e+00
[141,] 9.104921e-01 0.96659745 0.64754879 1.000000e+00
[142,] 9.993155e-01 0.99985174 0.66982670 1.000000e+00
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[1954,] 6.255521e-02 0.28692197 0.19221649 1.000000e+00
[1955,] 6.229022e-02 0.28617391 0.19171535 1.000000e+00
[1956,] 2.248644e-01 0.53039172 0.35532322 1.000000e+00
[1957,] 7.256183e-01 0.89537174 0.59983283 1.000000e+00
[1958,] 8.533754e-02 0.33921151 0.22724662 1.000000e+00
[1959,] 4.042366e-01 0.68894086 0.46153941 1.000000e+00
[1960,] 4.961956e-01 0.75260287 0.50418825 1.000000e+00
[1961,] 1.999905e-01 0.50636581 0.33922764 1.000000e+00
[1962,] 7.255521e-05 0.01882353 0.01261037 1.639181e-03
[1963,] 2.417918e-01 0.54398017 0.36442647 1.000000e+00
[1964,] 6.296246e-01 0.84006313 0.56278016 1.000000e+00
[1965,] 8.557161e-01 0.94681326 0.63429485 1.000000e+00
[1966,] 4.627161e-01 0.72758433 0.48742768 1.000000e+00
[1967,] 5.713344e-01 0.80387483 0.53853667 1.000000e+00
[1968,] 8.326719e-01 0.93833037 0.62861194 1.000000e+00
[1969,] 9.361798e-01 0.98020806 0.65666689 1.000000e+00
[1970,] 5.002492e-01 0.75498099 0.50578141 1.000000e+00
[1971,] 9.247382e-01 0.97393023 0.65246121 1.000000e+00
[1972,] 4.516120e-01 0.71929719 0.48187591 1.000000e+00
[1973,] 8.237666e-01 0.93524884 0.62654754 1.000000e+00
[1974,] 5.808360e-01 0.81112335 0.54339264 1.000000e+00
[1975,] 1.325584e-01 0.42105210 0.28207376 1.000000e+00
[1976,] 5.533091e-01 0.79366063 0.53169391 1.000000e+00
[1977,] 7.155836e-01 0.89416994 0.59902772 1.000000e+00
[1978,] 9.397855e-01 0.98140270 0.65746721 1.000000e+00
[1979,] 1.476940e-01 0.44252363 0.29645810 1.000000e+00
[1980,] 8.004921e-01 0.92692868 0.62097364 1.000000e+00
[1981,] 5.615142e-04 0.03455882 0.02315186 1.268583e-02
[1982,] 2.959874e-01 0.59529785 0.39880552 1.000000e+00
[1983,] 6.649590e-01 0.86028968 0.57633045 1.000000e+00
[1984,] 5.302082e-01 0.77396869 0.51850177 1.000000e+00
[1985,] 6.827129e-02 0.29800550 0.19964164 1.000000e+00
[1986,] 4.763975e-01 0.73877751 0.49492628 1.000000e+00
[1987,] 1.597413e-01 0.45678990 0.30601544 1.000000e+00
[1988,] 3.069306e-01 0.60395407 0.40460455 1.000000e+00
[1989,] 7.948044e-01 0.92617045 0.62046569 1.000000e+00
[1990,] 4.470032e-03 0.08321637 0.05574881 1.009878e-01
[1991,] 3.266972e-01 0.62125375 0.41619406 1.000000e+00
[1992,] 2.979685e-01 0.59744466 0.40024372 1.000000e+00
[1993,] 1.767445e-01 0.48021404 0.32170788 1.000000e+00
[1994,] 8.755205e-01 0.95565382 0.64021737 1.000000e+00
[1995,] 8.743281e-01 0.95565382 0.64021737 1.000000e+00
[1996,] 7.030789e-01 0.88901476 0.59557412 1.000000e+00
[1997,] 5.974164e-01 0.82268028 0.55113493 1.000000e+00
[1998,] 9.733943e-01 0.99107223 0.66394508 1.000000e+00
[1999,] 8.862744e-01 0.95723680 0.64127784 1.000000e+00
[2000,] 8.267634e-01 0.93642169 0.62733326 1.000000e+00
[2001,] 6.501356e-01 0.85127220 0.57028940 1.000000e+00
[2002,] 9.695962e-01 0.99107223 0.66394508 1.000000e+00
[2003,] 4.439748e-01 0.71623410 0.47982386 1.000000e+00
[2004,] 8.604795e-01 0.95075636 0.63693643 1.000000e+00
[2005,] 7.677256e-01 0.91597818 0.61363762 1.000000e+00
[2006,] 4.576151e-01 0.72423365 0.48518297 1.000000e+00
[2007,] 1.411230e-01 0.43377176 0.29059499 1.000000e+00
[2008,] 5.194006e-02 0.26673667 0.17869384 1.000000e+00
[2009,] 2.669180e-01 0.56413724 0.37793022 1.000000e+00
[2010,] 9.528013e-01 0.98399414 0.65920328 1.000000e+00
[2011,] 1.467319e-01 0.44130930 0.29564458 1.000000e+00
[2012,] 7.263785e-01 0.89553225 0.59994036 1.000000e+00
[2013,] 9.926183e-01 0.99654430 0.66761097 1.000000e+00
[2014,] 8.684227e-01 0.95309713 0.63850457 1.000000e+00
[2015,] 7.732492e-01 0.91832210 0.61520787 1.000000e+00
[2016,] 7.101830e-01 0.89085443 0.59680657 1.000000e+00
[2017,] 9.540757e-01 0.98416721 0.65931923 1.000000e+00
[2018,] 1.671009e-01 0.46756399 0.31323329 1.000000e+00
[2019,] 2.270126e-01 0.53109225 0.35579252 1.000000e+00
[2020,] 8.240221e-01 0.93524884 0.62654754 1.000000e+00
[2021,] 2.910631e-01 0.58694020 0.39320652 1.000000e+00
[2022,] 8.042145e-01 0.92737723 0.62127414 1.000000e+00
[2023,] 2.910410e-02 0.20108932 0.13471497 6.575253e-01
[2024,] 8.904385e-01 0.95977219 0.64297637 1.000000e+00
[2025,] 3.376309e-01 0.63181228 0.42326749 1.000000e+00
[2026,] 7.617382e-01 0.91415437 0.61241580 1.000000e+00
[2027,] 4.794953e-04 0.03276596 0.02195077 1.083285e-02
[2028,] 3.812050e-01 0.67016602 0.44896166 1.000000e+00
[2029,] 4.959306e-02 0.26044702 0.17448024 1.000000e+00
[2030,] 2.563091e-02 0.18895349 0.12658486 5.790584e-01
[2031,] 7.640252e-01 0.91499622 0.61297978 1.000000e+00
[2032,] 6.732334e-01 0.86472853 0.57930414 1.000000e+00
[2033,] 4.315457e-03 0.08240964 0.05520836 9.749562e-02
[2034,] 5.554196e-01 0.79462128 0.53233748 1.000000e+00
[2035,] 4.422902e-01 0.71623218 0.47982258 1.000000e+00
[2036,] 5.806656e-01 0.81112335 0.54339264 1.000000e+00
[2037,] 3.239274e-01 0.62045317 0.41565773 1.000000e+00
[2038,] 8.175773e-01 0.93462676 0.62613079 1.000000e+00
[2039,] 1.518423e-01 0.45111528 0.30221386 1.000000e+00
[2040,] 7.014543e-01 0.88766866 0.59467234 1.000000e+00
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[2080,] 4.106309e-02 0.24053407 0.16114003 9.277050e-01
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[2082,] 3.593975e-01 0.65326261 0.43763763 1.000000e+00
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[3170,] 1.792114e-02 0.16324713 0.10936350 4.048776e-01
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