Compute mr.mash-RSS TWAS weights from summary statistics
Source:R/regularizedRegressionWrappers.R
mrmashRssWeights.RdMulti-context summary-statistics analog of mrmashWeights:
extracts coefficients from an existing mr.mashr::mr.mash.rss fit, or
fits one from stat (variants x conditions) and LD.
Usage
mrmashRssWeights(
stat,
LD,
mrmashRssFit = NULL,
dataDrivenPriorMatrices = NULL,
canonicalPriorMatrices = TRUE,
S0 = NULL,
w0 = NULL,
V = NULL,
covY = NULL,
retainFit = FALSE,
fitDetail = c("slim", "full"),
...
)Arguments
- stat
A list with
z(variants x conditions matrix) andn(per-context numeric vector or scalar). May also includeBhat,Shatmatrices.- LD
LD correlation matrix.
- mrmashRssFit
Optional pre-fitted
mr.mash.rssobject; skips fitting when supplied.- dataDrivenPriorMatrices
Optional list with element
U(list of raw covariance matrices). Passed directly tomr.mashr::expand_covs()alongside the canonical mixture.- canonicalPriorMatrices
Logical. When TRUE (default), include the standard canonical mixture from
mr.mashr::compute_canonical_covs(). When FALSE,dataDrivenPriorMatricesmust be supplied.- S0
Optional pre-built list of prior covariance matrices, bypassing the canonical / data-driven construction.
- w0
Optional prior mixture weights; defaults to
computeW0(Bhat, length(S0)).- V
Optional residual covariance matrix (K x K). When NULL, defaults to the identity matrix of size K.
- covY
Optional response covariance matrix (K x K). When NULL, defaults to the identity matrix of size K.
- retainFit
If TRUE, attaches (as the
"fit"attribute on the returned weights) the inputsfineMappingPipelineneeds to rebuild the mvSuSiE reweighted prior:dataDrivenPriorMatrices, the fittedw0, and the fittedV. Default FALSE.- fitDetail
How much to retain when
retainFit = TRUE."slim"(default) keeps only those reconstruction inputs (the coefficients are already the returned weights);"full"additionally keeps the completemr.mash.rssfit under$fit. MirrorsmrmashWeights.- ...
Additional arguments forwarded to
mr.mashr::mr.mash.rss.
Details
Follows the *_rss_weights(stat, LD, ...) contract. Expects
stat$z to be a numeric matrix (variants x conditions) and
stat$n a per-context numeric vector or scalar. stat$Bhat and
stat$Shat are used if present; otherwise derived from Z and n.
Prior construction reuses the same infrastructure as the individual-level
mrmashWrapper: computeGrid +
mr.mashr::compute_canonical_covs() + mr.mashr::expand_covs()
for S0, and computeW0 for the mixture weights. Supply
dataDrivenPriorMatrices (e.g. from computeCovFlash /
computeCovDiag) to add data-driven covariance components
alongside the canonical mixture.
Examples
data(eqtlRegionExample)
data(multiTraitData)
X <- eqtlRegionExample$X[, 1:30]
cond <- c("brain", "blood", "muscle")
zmat <- matrix(rnorm(30 * 3), 30, 3,
dimnames = list(colnames(X), cond))
stat <- list(z = zmat, n = matrix(nrow(X), 30, 3))
mrmashRssWeights(stat, cor(X),
dataDrivenPriorMatrices = multiTraitData$priorMatrices,
canonicalPriorMatrices = TRUE)
#> Warning: STATS is longer than the extent of 'dim(x)[MARGIN]'
#> Warning: data length differs from size of matrix: [2700 != 30 x 3]
#> Processing the inputs... Done!
#> Fitting the optimization algorithm using 4 RcppParallel threads...
#> iter mu1_max.diff ELBO_diff ELBO
#> 1 1.28e-01 Inf -1.78169220247537805335e+03
#> 2 1.05e-01 1.48e+01 -1.76684785898449945307e+03
#> 3 9.09e-02 8.85e+00 -1.75799853589070630733e+03
#> 4 9.63e-02 1.20e+01 -1.74598631953117887861e+03
#> 5 1.09e-01 1.48e+01 -1.73115095133780073411e+03
#> 6 1.14e-01 1.70e+01 -1.71417331704085927413e+03
#> 7 1.16e-01 1.88e+01 -1.69542263843319233274e+03
#> 8 1.14e-01 2.02e+01 -1.67520615899520544190e+03
#> 9 1.09e-01 2.22e+01 -1.65297988640483185918e+03
#> 10 1.10e-01 2.18e+01 -1.63113941335413187517e+03
#> 11 1.07e-01 2.04e+01 -1.61073548233982069178e+03
#> 12 1.02e-01 1.91e+01 -1.59162381315432799056e+03
#> 13 9.40e-02 1.80e+01 -1.57365572359011594017e+03
#> 14 9.45e-02 1.75e+01 -1.55617278244422095668e+03
#> 15 1.01e-01 1.72e+01 -1.53898259897388811623e+03
#> 16 1.04e-01 1.62e+01 -1.52273353669102107233e+03
#> 17 1.02e-01 1.49e+01 -1.50783136701313424055e+03
#> 18 9.78e-02 1.36e+01 -1.49418274757345648140e+03
#> 19 9.39e-02 1.27e+01 -1.48146958157201243012e+03
#> 20 9.03e-02 1.19e+01 -1.46956769758539530812e+03
#> 21 8.71e-02 1.09e+01 -1.45871151418896943142e+03
#> 22 8.41e-02 9.74e+00 -1.44897026290725784747e+03
#> 23 8.11e-02 8.73e+00 -1.44023554401503974987e+03
#> 24 7.75e-02 7.87e+00 -1.43236472476858716618e+03
#> 25 7.36e-02 7.11e+00 -1.42525235617827979695e+03
#> 26 6.95e-02 6.43e+00 -1.41882012161993543486e+03
#> 27 6.54e-02 5.82e+00 -1.41300104528668111925e+03
#> 28 6.14e-02 5.27e+00 -1.40773468973302078666e+03
#> 29 5.76e-02 4.77e+00 -1.40296585572796584529e+03
#> 30 5.38e-02 4.32e+00 -1.39864320950662181531e+03
#> 31 5.01e-02 3.93e+00 -1.39471658877740128446e+03
#> 32 4.64e-02 3.59e+00 -1.39113074850284374406e+03
#> 33 4.42e-02 3.32e+00 -1.38780823717281759855e+03
#> 34 4.55e-02 3.20e+00 -1.38460899550236081268e+03
#> 35 4.91e-02 3.27e+00 -1.38133927694494150273e+03
#> 36 5.27e-02 3.31e+00 -1.37802551453928435876e+03
#> 37 5.13e-02 3.10e+00 -1.37492340576634160243e+03
#> 38 4.79e-02 2.81e+00 -1.37210864985611624434e+03
#> 39 4.49e-02 2.55e+00 -1.36955725422039245132e+03
#> 40 4.22e-02 2.31e+00 -1.36724332418708786463e+03
#> 41 3.97e-02 2.10e+00 -1.36514270739553535350e+03
#> 42 3.73e-02 1.91e+00 -1.36322961338625418648e+03
#> 43 3.50e-02 1.77e+00 -1.36146057067426363574e+03
#> 44 3.49e-02 1.87e+00 -1.35958690971986516161e+03
#> 45 9.30e-02 4.77e+00 -1.35481530784159849645e+03
#> 46 3.69e-02 3.60e+00 -1.35121370793258847698e+03
#> 47 3.47e-02 1.94e+00 -1.34927103100450494821e+03
#> 48 3.49e-02 1.74e+00 -1.34752728049639677010e+03
#> 49 3.44e-02 1.62e+00 -1.34591172944018444468e+03
#> 50 3.51e-02 1.50e+00 -1.34441619392347251960e+03
#> 51 3.54e-02 1.38e+00 -1.34303577812861885832e+03
#> 52 3.51e-02 1.27e+00 -1.34176620720961568622e+03
#> 53 3.46e-02 1.16e+00 -1.34060186078323022230e+03
#> 54 3.38e-02 1.07e+00 -1.33953647046929972930e+03
#> 55 3.27e-02 9.73e-01 -1.33856393056364640870e+03
#> 56 3.14e-02 8.85e-01 -1.33767878235024886635e+03
#> 57 2.97e-02 8.02e-01 -1.33687651544367645329e+03
#> 58 2.76e-02 7.23e-01 -1.33615373019956859935e+03
#> 59 2.69e-02 6.46e-01 -1.33550782260761593534e+03
#> 60 2.63e-02 5.73e-01 -1.33493476586233828129e+03
#> 61 2.57e-02 5.13e-01 -1.33442136148440476973e+03
#> 62 2.51e-02 4.89e-01 -1.33393194700161120636e+03
#> 63 2.84e-02 5.10e-01 -1.33342192669948826733e+03
#> 64 3.00e-02 5.31e-01 -1.33289060755980267459e+03
#> 65 2.93e-02 5.41e-01 -1.33234996406592335916e+03
#> 66 2.79e-02 6.06e-01 -1.33174395319624454714e+03
#> 67 3.61e-02 8.27e-01 -1.33091657757219218183e+03
#> 68 4.67e-02 1.10e+00 -1.32981228543333418202e+03
#> 69 5.04e-02 1.19e+00 -1.32862444604398001502e+03
#> 70 5.13e-02 1.18e+00 -1.32744292511304183790e+03
#> 71 5.06e-02 1.15e+00 -1.32628946257484176385e+03
#> 72 4.90e-02 1.08e+00 -1.32521283322668023175e+03
#> 73 4.71e-02 9.82e-01 -1.32423087710683671503e+03
#> 74 4.50e-02 8.90e-01 -1.32334069638750406739e+03
#> 75 4.28e-02 8.05e-01 -1.32253587037247075386e+03
#> 76 4.07e-02 7.26e-01 -1.32180951493180555190e+03
#> 77 3.86e-02 6.55e-01 -1.32115480885180022597e+03
#> 78 3.65e-02 5.90e-01 -1.32056522849040220535e+03
#> 79 3.45e-02 5.31e-01 -1.32003466937529537972e+03
#> 80 3.26e-02 4.77e-01 -1.31955749354668887463e+03
#> 81 3.08e-02 4.29e-01 -1.31912853298571758387e+03
#> 82 2.91e-02 3.85e-01 -1.31874307068774487561e+03
#> 83 2.74e-02 3.46e-01 -1.31839681226534003144e+03
#> 84 2.58e-02 3.11e-01 -1.31808585477422479926e+03
#> 85 2.42e-02 2.79e-01 -1.31780665582451797491e+03
#> 86 2.28e-02 2.51e-01 -1.31755600419158054137e+03
#> 87 2.14e-02 2.25e-01 -1.31733099230384118528e+03
#> 88 2.00e-02 2.02e-01 -1.31712899064690464002e+03
#> 89 1.88e-02 1.81e-01 -1.31694762400513718603e+03
#> 90 1.76e-02 1.63e-01 -1.31678474943148830789e+03
#> 91 1.64e-02 1.46e-01 -1.31663843583632365153e+03
#> 92 1.53e-02 1.31e-01 -1.31650694509451523118e+03
#> 93 1.43e-02 1.18e-01 -1.31638871457890809324e+03
#> 94 1.33e-02 1.06e-01 -1.31628234103553199930e+03
#> 95 1.24e-02 9.58e-02 -1.31618656572152349327e+03
#> 96 1.16e-02 8.63e-02 -1.31610026073071230712e+03
#> 97 1.07e-02 7.78e-02 -1.31602241643491629475e+03
#> 98 9.95e-03 7.03e-02 -1.31595212997154794721e+03
#> 99 9.23e-03 6.35e-02 -1.31588859471043610938e+03
#> 100 8.54e-03 5.75e-02 -1.31583109063475649236e+03
#> 101 7.89e-03 5.21e-02 -1.31577897557340361345e+03
#> 102 7.45e-03 4.73e-02 -1.31573167722421385406e+03
#> 103 7.16e-03 4.30e-02 -1.31568868591005184498e+03
#> 104 6.88e-03 3.91e-02 -1.31564954801218891589e+03
#> 105 6.60e-03 3.57e-02 -1.31561386002813969753e+03
#> 106 6.33e-03 3.26e-02 -1.31558126320384599239e+03
#> 107 6.06e-03 2.98e-02 -1.31555143869282892410e+03
#> 108 5.80e-03 2.73e-02 -1.31552410319781211001e+03
#> 109 5.55e-03 2.51e-02 -1.31549900505305186016e+03
#> 110 5.30e-03 2.31e-02 -1.31547592070837163192e+03
#> 111 5.06e-03 2.13e-02 -1.31545465157862486194e+03
#> 112 4.83e-03 1.96e-02 -1.31543502122488962414e+03
#> 113 4.60e-03 1.81e-02 -1.31541687283619421578e+03
#> 114 4.38e-03 1.68e-02 -1.31540006698308980049e+03
#> 115 4.16e-03 1.56e-02 -1.31538447961650263096e+03
#> 116 3.95e-03 1.45e-02 -1.31537000028770535209e+03
#> 117 3.74e-03 1.35e-02 -1.31535653056701471542e+03
#> 118 3.54e-03 1.25e-02 -1.31534398264106562237e+03
#> 119 3.34e-03 1.17e-02 -1.31533227807000594112e+03
#> 120 3.15e-03 1.09e-02 -1.31532134668788921772e+03
#> 121 2.97e-03 1.02e-02 -1.31531112563088800016e+03
#> 122 2.79e-03 9.57e-03 -1.31530155847957712467e+03
#> 123 2.62e-03 8.96e-03 -1.31529259450272002141e+03
#> 124 2.45e-03 8.41e-03 -1.31528418799130554362e+03
#> 125 2.29e-03 7.89e-03 -1.31527629767265511873e+03
#> 126 2.31e-03 7.41e-03 -1.31526888619551982629e+03
#> 127 2.33e-03 6.97e-03 -1.31526191967789668524e+03
#> 128 2.34e-03 6.55e-03 -1.31525536731032798343e+03
#> 129 2.35e-03 6.17e-03 -1.31524920100805229595e+03
#> 130 2.35e-03 5.81e-03 -1.31524339510622326088e+03
#> 131 2.35e-03 5.47e-03 -1.31523792609293968781e+03
#> 132 2.35e-03 5.15e-03 -1.31523277237550109930e+03
#> 133 2.34e-03 4.86e-03 -1.31522791407574845834e+03
#> 134 2.32e-03 4.58e-03 -1.31522333285092167898e+03
#> 135 2.31e-03 4.32e-03 -1.31521901173670107710e+03
#> 136 2.29e-03 4.08e-03 -1.31521493500975293500e+03
#> 137 2.26e-03 3.85e-03 -1.31521108806713436934e+03
#> 138 2.24e-03 3.63e-03 -1.31520745732046975718e+03
#> 139 2.21e-03 3.43e-03 -1.31520403010291965984e+03
#> 140 2.18e-03 3.24e-03 -1.31520079458727741439e+03
#> 141 2.15e-03 3.05e-03 -1.31519773971370204890e+03
#> 142 2.11e-03 2.88e-03 -1.31519485512582991760e+03
#> 143 2.07e-03 2.72e-03 -1.31519213111413478146e+03
#> 144 2.03e-03 2.57e-03 -1.31518955856554202910e+03
#> 145 1.99e-03 2.43e-03 -1.31518712891851419045e+03
#> 146 1.95e-03 2.29e-03 -1.31518483412281693745e+03
#> 147 1.91e-03 2.17e-03 -1.31518266660336644236e+03
#> 148 1.86e-03 2.05e-03 -1.31518061922763422444e+03
#> 149 1.82e-03 1.93e-03 -1.31517868527611835816e+03
#> 150 1.77e-03 1.83e-03 -1.31517685841549132419e+03
#> 151 1.73e-03 1.73e-03 -1.31517513267407412059e+03
#> 152 1.68e-03 1.63e-03 -1.31517350241938083855e+03
#> 153 1.63e-03 1.54e-03 -1.31517196233743106859e+03
#> 154 1.58e-03 1.45e-03 -1.31517050741366301736e+03
#> 155 1.53e-03 1.37e-03 -1.31516913291524565466e+03
#> 156 1.48e-03 1.30e-03 -1.31516783437463300288e+03
#> 157 1.44e-03 1.23e-03 -1.31516660757425529482e+03
#> 158 1.39e-03 1.16e-03 -1.31516544853218465505e+03
#> 159 1.34e-03 1.10e-03 -1.31516435348875393174e+03
#> 160 1.29e-03 1.03e-03 -1.31516331889397656596e+03
#> 161 1.24e-03 9.77e-04 -1.31516234139572179629e+03
#> 162 1.19e-03 9.24e-04 -1.31516141782860813692e+03
#> 163 1.15e-03 8.73e-04 -1.31516054520353827684e+03
#> 164 1.10e-03 8.25e-04 -1.31515972069783629195e+03
#> 165 1.05e-03 7.79e-04 -1.31515894164592486959e+03
#> 166 1.01e-03 7.36e-04 -1.31515820553055414166e+03
#> 167 9.60e-04 6.96e-04 -1.31515750997450936666e+03
#> 168 9.15e-04 6.57e-04 -1.31515685273277517808e+03
#> 169 8.71e-04 6.21e-04 -1.31515623168515094221e+03
#> 170 8.27e-04 5.87e-04 -1.31515564482927493373e+03
#> 171 7.85e-04 5.55e-04 -1.31515509027399957631e+03
#> 172 7.43e-04 5.24e-04 -1.31515456623320869767e+03
#> 173 7.31e-04 4.95e-04 -1.31515407101990899719e+03
#> 174 7.28e-04 4.68e-04 -1.31515360304069531594e+03
#> 175 7.25e-04 4.42e-04 -1.31515316079050535336e+03
#> 176 7.20e-04 4.18e-04 -1.31515274284767133395e+03
#> 177 7.14e-04 3.95e-04 -1.31515234786927658206e+03
#> 178 7.07e-04 3.73e-04 -1.31515197458672855646e+03
#> 179 6.99e-04 3.53e-04 -1.31515162180161587457e+03
#> 180 6.90e-04 3.33e-04 -1.31515128838177906800e+03
#> 181 6.81e-04 3.15e-04 -1.31515097325764554625e+03
#> 182 6.70e-04 2.98e-04 -1.31515067541870894274e+03
#> 183 6.59e-04 2.82e-04 -1.31515039391024811266e+03
#> 184 6.47e-04 2.66e-04 -1.31515012783024803866e+03
#> 185 6.35e-04 2.52e-04 -1.31514987632644442783e+03
#> 186 6.22e-04 2.38e-04 -1.31514963859358476839e+03
#> 187 6.09e-04 2.25e-04 -1.31514941387082080837e+03
#> 188 5.95e-04 2.12e-04 -1.31514920143925519369e+03
#> 189 5.81e-04 2.01e-04 -1.31514900061961179745e+03
#> 190 5.66e-04 1.90e-04 -1.31514881077007930799e+03
#> 191 5.51e-04 1.79e-04 -1.31514863128422916816e+03
#> 192 5.36e-04 1.70e-04 -1.31514846158907130302e+03
#> 193 5.21e-04 1.60e-04 -1.31514830114322649024e+03
#> 194 5.06e-04 1.52e-04 -1.31514814943519286317e+03
#> 195 4.90e-04 1.43e-04 -1.31514800598170609192e+03
#> 196 4.74e-04 1.36e-04 -1.31514787032619824458e+03
#> 197 4.59e-04 1.28e-04 -1.31514774203733668401e+03
#> 198 4.43e-04 1.21e-04 -1.31514762070765164026e+03
#> 199 4.27e-04 1.15e-04 -1.31514750595223085838e+03
#> 200 4.11e-04 1.09e-04 -1.31514739740747882024e+03
#> 201 3.96e-04 1.03e-04 -1.31514729472997532866e+03
#> 202 3.80e-04 9.71e-05 -1.31514719759536797028e+03
#> 203 3.65e-04 9.19e-05 -1.31514710569732369549e+03
#> 204 3.50e-04 8.70e-05 -1.31514701874655111169e+03
#> 205 3.34e-04 8.23e-05 -1.31514693646987507236e+03
#> 206 3.19e-04 7.79e-05 -1.31514685860935583150e+03
#> 207 3.05e-04 7.37e-05 -1.31514678492144457778e+03
#> 208 2.90e-04 6.97e-05 -1.31514671517620945451e+03
#> 209 2.76e-04 6.60e-05 -1.31514664915658704558e+03
#> 210 2.62e-04 6.25e-05 -1.31514658665766683043e+03
#> 211 2.50e-04 5.92e-05 -1.31514652748602702559e+03
#> 212 2.39e-04 5.60e-05 -1.31514647145910112158e+03
#> 213 2.27e-04 5.31e-05 -1.31514641840458193656e+03
#> 214 2.16e-04 5.02e-05 -1.31514636815984749774e+03
#> 215 2.05e-04 4.76e-05 -1.31514632057141943733e+03
#> 216 1.94e-04 4.51e-05 -1.31514627549446095145e+03
#> 217 1.83e-04 4.27e-05 -1.31514623279229408581e+03
#> 218 1.72e-04 4.05e-05 -1.31514619233593452918e+03
#> 219 1.75e-04 3.83e-05 -1.31514615400366301401e+03
#> 220 1.76e-04 3.63e-05 -1.31514611768061649855e+03
#> 221 1.78e-04 3.44e-05 -1.31514608325840254111e+03
#> 222 1.79e-04 3.26e-05 -1.31514605063472254187e+03
#> 223 1.79e-04 3.09e-05 -1.31514601971303090977e+03
#> 224 1.79e-04 2.93e-05 -1.31514599040221264659e+03
#> 225 1.79e-04 2.78e-05 -1.31514596261625638363e+03
#> 226 1.79e-04 2.63e-05 -1.31514593627397925957e+03
#> 227 1.78e-04 2.50e-05 -1.31514591129873042519e+03
#> 228 1.77e-04 2.37e-05 -1.31514588761814138707e+03
#> 229 1.75e-04 2.25e-05 -1.31514586516387771553e+03
#> 230 1.74e-04 2.13e-05 -1.31514584387140166655e+03
#> 231 1.72e-04 2.02e-05 -1.31514582367974480803e+03
#> 232 1.70e-04 1.91e-05 -1.31514580453131475224e+03
#> 233 1.67e-04 1.82e-05 -1.31514578637168710884e+03
#> 234 1.65e-04 1.72e-05 -1.31514576914942063013e+03
#> 235 1.62e-04 1.63e-05 -1.31514575281589895894e+03
#> 236 1.59e-04 1.55e-05 -1.31514573732513963478e+03
#> 237 1.56e-04 1.47e-05 -1.31514572263365994331e+03
#> 238 1.53e-04 1.39e-05 -1.31514570870032184757e+03
#> 239 1.50e-04 1.32e-05 -1.31514569548620738715e+03
#> 240 1.47e-04 1.25e-05 -1.31514568295447315904e+03
#> 241 1.43e-04 1.19e-05 -1.31514567107023094650e+03
#> 242 1.40e-04 1.13e-05 -1.31514565980045745164e+03
#> 243 1.36e-04 1.07e-05 -1.31514564911386037238e+03
#> 244 1.33e-04 1.01e-05 -1.31514563898078495185e+03
#> 245 1.29e-04 9.61e-06 -1.31514562937313348812e+03
#> 246 1.25e-04 9.11e-06 -1.31514562026426210650e+03
#> 247 1.21e-04 8.64e-06 -1.31514561162890049673e+03
#> 248 1.18e-04 8.19e-06 -1.31514560344308119966e+03
#> 249 1.14e-04 7.76e-06 -1.31514559568406002654e+03
#> 250 1.10e-04 7.35e-06 -1.31514558833025785134e+03
#> 251 1.06e-04 6.97e-06 -1.31514558136117261711e+03
#> 252 1.02e-04 6.60e-06 -1.31514557475735045955e+03
#> 253 9.84e-05 6.26e-06 -1.31514556850030999158e+03
#> Done!
#> Processing the outputs... Done!
#> mr.mash.rss successfully executed in 0.03876048 minutes!
#> brain blood muscle
#> chr22:32119788:T:C 4.538404e-05 6.875414e-05 -1.1796408286
#> chr22:32119867:T:G -5.393463e-04 -2.869525e-03 1.5124048189
#> chr22:32119961:T:G 2.238199e+00 1.232415e-03 -0.0022922301
#> chr22:32120053:T:C 1.090823e-03 -2.333399e-03 1.1271891703
#> chr22:32120593:A:G 3.051221e-04 -2.640063e-06 -0.5775848398
#> chr22:32120636:T:C -2.583248e+00 -1.860793e+00 1.2052623320
#> chr22:32120932:G:A 1.312885e-04 1.215957e-03 -0.0890315231
#> chr22:32120975:A:G 1.329311e+00 1.329311e+00 1.3293115541
#> chr22:32121290:C:T -9.993271e-03 -6.316359e-03 0.0197818565
#> chr22:32121498:A:C 2.730969e+00 1.492493e+00 -0.8023967754
#> chr22:32121635:T:G 8.935833e-01 -5.274719e-04 0.0005677665
#> chr22:32121702:A:G -2.363450e-02 -1.533756e-02 -0.0031764719
#> chr22:32121936:G:A 3.480121e-04 -7.874398e-05 2.3625711938
#> chr22:32122351:A:G -5.655109e-05 1.174140e-03 -1.3994302130
#> chr22:32122676:A:G -4.308276e-04 -2.076459e-03 -0.5678069836
#> chr22:32123055:A:G -3.541488e-03 -2.754130e-03 -2.4913916268
#> chr22:32123164:T:C 8.248168e-05 2.339598e-03 0.5139664845
#> chr22:32123383:T:C 1.421188e-05 4.299820e-05 0.4910593411
#> chr22:32123461:T:C 8.551042e-03 4.286133e-02 0.0080797271
#> chr22:32123806:C:T -4.096131e-04 2.568892e-03 2.5608938550
#> chr22:32124049:G:A 1.006152e+00 2.269772e-03 0.0016838975
#> chr22:32124126:C:T 2.549026e+00 -3.926094e-04 0.0002857932
#> chr22:32124147:A:C -1.555803e+00 -1.555803e+00 -1.5558026914
#> chr22:32124381:G:A 1.656585e+00 -4.231853e-04 0.0013046209
#> chr22:32124644:A:G 1.283351e-04 1.319783e-05 -2.1960378475
#> chr22:32124683:T:C -8.966490e-02 8.591800e-01 -0.7853498509
#> chr22:32124952:C:A 1.240320e+00 1.368477e+00 -0.9339191406
#> chr22:32125308:A:G 2.405842e-02 7.067686e-03 -0.0398038297
#> chr22:32125638:A:C 2.321553e-02 7.586655e-03 -0.2730928052
#> chr22:32125730:G:A 5.319382e-03 -1.376405e-02 -0.0087497759