Extracts coefficients from an existing mr.mash fit or fits mr.mash from `X` and `Y`.
Usage
mrmashWeights(
mrmashFit = NULL,
X = NULL,
Y = NULL,
fitRetention = c("none", "slim", "full"),
dataDrivenPriorMatrices = NULL,
methodArgs = MrmashOptions()
)Arguments
- mrmashFit
Optional fitted mr.mash object.
- X
Genotype matrix. Required when `mrmashFit` is NULL.
- Y
Phenotype matrix. Required when `mrmashFit` is NULL.
- fitRetention
How much of the mr.mash fit is kept as the
"fit"attribute of the returned weights."none"(default) attaches nothing."slim"keeps whatfineMappingPipelineneeds to rebuild the mvSuSiE reweighted mixture prior and residual variance — the originaldataDrivenPriorMatrices, the fittedw0andV; the heavy coefficient matrixmu1is already returned as the weights, so it is not duplicated."full"additionally retains the complete fit under$fit, at the cost of a larger payload.- dataDrivenPriorMatrices
Optional list of data-driven prior covariance matrices; forwarded to
mrmashWrapperwhen it has to fit, and retained in the payload for mvSuSiE prior reconstruction.- methodArgs
Options forwarded to
mr.mashr::mr.mash, built withMrmashOptions. A bare list is refused: it cannot be checked against the engine, so a misspelled option would be silently ignored.
Examples
data(multiTraitData)
X <- multiTraitData$X[, 1:60]
Y <- multiTraitData$Y
ddpm <- multiTraitData$priorMatrices
fit <- mrmashWrapper(X = X, Y = Y, dataDrivenPriorMatrices = ddpm,
prior = MrmashPriorParam(canonicalPriorMatrices = TRUE))
mrmashWeights(mrmashFit = fit, X = X, Y = Y)
#> cond_1 cond_2 cond_3
#> chr8:27119632_TA_T 5.561157e-05 4.353552e-05 5.882309e-05
#> chr8:27119646_A_AG 3.091589e-05 1.402586e-04 -2.235102e-05
#> chr8:27119646_A_G 9.560354e-06 4.757901e-05 -5.146408e-05
#> chr8:27119788_C_T 8.471383e-05 6.740792e-05 -2.154474e-05
#> chr8:27119867_G_T 8.472866e-05 6.742221e-05 -2.154701e-05
#> chr8:27119961_G_T 1.259163e-04 2.154958e-04 2.590358e-04
#> chr8:27120636_C_T -1.811401e-05 -1.386416e-04 -1.557291e-04
#> chr8:27120932_A_G 1.151670e-04 4.785297e-05 -6.201110e-05
#> chr8:27121290_T_C 3.662632e-05 1.738812e-04 -5.609926e-05
#> chr8:27121498_C_A 3.663368e-05 1.739231e-04 -5.609879e-05
#> chr8:27121702_G_A 3.724500e-05 1.412913e-04 8.994980e-05
#> chr8:27121936_A_G 9.556160e-06 4.759476e-05 -5.147337e-05
#> chr8:27122117_CAA_C 1.723840e-05 2.475239e-04 9.116128e-05
#> chr8:27122117_CAAA_C 6.841359e-05 1.976078e-06 -1.005971e-04
#> chr8:27122139_A_C 9.079583e-05 1.689728e-04 2.328842e-04
#> chr8:27122351_G_A 4.157063e-05 1.794141e-04 -6.555982e-05
#> chr8:27123070_G_C 3.551801e-05 7.676549e-05 -1.576414e-04
#> chr8:27123164_C_T 7.587637e-06 3.150173e-05 -1.000834e-04
#> chr8:27123274_T_TG 1.308465e-04 2.105558e-04 2.719221e-04
#> chr8:27123283_T_TTTTTGTTTTGTTTTG -5.253190e-05 -1.094583e-04 -2.245266e-04
#> chr8:27123283_T_TTTTTGTTTTG 9.317361e-05 1.465886e-04 1.583357e-05
#> chr8:27123283_T_TTTTTGTTTTGTTTTGTTTTG -5.950334e-05 1.644634e-04 3.194985e-05
#> chr8:27123383_C_T 3.583511e-05 8.445032e-05 -1.489388e-04
#> chr8:27123630_G_C 2.284435e-05 6.511778e-05 -1.630939e-04
#> chr8:27123806_T_C 3.583813e-05 8.447227e-05 -1.489869e-04
#> chr8:27124049_A_G 3.584106e-05 8.448532e-05 -1.490090e-04
#> chr8:27124126_T_C -1.816144e-05 -1.387204e-04 -1.558414e-04
#> chr8:27124147_C_A 3.584089e-05 8.448830e-05 -1.490432e-04
#> chr8:27124381_A_G -9.121265e-05 -2.123641e-04 1.268456e-05
#> chr8:27124644_G_A 9.544141e-06 4.762289e-05 -5.154593e-05
#> chr8:27124683_C_T -1.817219e-05 -1.387474e-04 -1.558845e-04
#> chr8:27125591_C_G -9.123199e-05 -2.124090e-04 1.268015e-05
#> chr8:27125730_A_G 9.432441e-06 1.756418e-04 1.517393e-04
#> chr8:27125829_T_A -8.776534e-05 -2.067139e-04 1.851120e-05
#> chr8:27126386_A_G -2.021173e-05 -2.999509e-05 -2.688315e-04
#> chr8:27126486_C_T 9.547449e-06 4.763605e-05 -5.155878e-05
#> chr8:27127215_T_A 3.647886e-05 1.569378e-04 -2.510399e-05
#> chr8:27127370_T_C -8.032067e-05 -1.570609e-04 -1.062575e-05
#> chr8:27127374_T_C -8.033725e-05 -1.570895e-04 -1.063530e-05
#> chr8:27127405_T_C 9.553130e-06 4.764787e-05 -5.155805e-05
#> chr8:27128069_G_A 3.586610e-05 8.455903e-05 -1.491277e-04
#> chr8:27128102_T_TAAAG 2.770459e-05 7.261775e-05 -1.722385e-04
#> chr8:27128473_C_G 1.322068e-04 1.967175e-04 2.814321e-04
#> chr8:27128733_G_T -1.819553e-05 -1.387913e-04 -1.559689e-04
#> chr8:27129375_G_GA 3.584232e-05 8.453960e-05 -1.492360e-04
#> chr8:27129602_T_C 2.809430e-05 8.742965e-05 -1.721622e-04
#> chr8:27129674_A_G 3.584601e-05 8.456538e-05 -1.492865e-04
#> chr8:27129849_TAAA_T 1.407135e-04 2.028497e-04 2.891943e-04
#> chr8:27129864_G_A 8.801942e-05 1.421412e-04 2.335309e-04
#> chr8:27129921_C_T 8.937974e-05 2.276729e-04 1.154284e-04
#> chr8:27130038_G_A 1.324769e-04 1.970244e-04 2.818949e-04
#> chr8:27130250_G_C -9.808644e-05 -1.830013e-04 3.437385e-06
#> chr8:27130586_G_C 3.578302e-05 8.448718e-05 -1.494439e-04
#> chr8:27130820_A_T 3.644281e-05 1.569637e-04 -2.525233e-05
#> chr8:27131153_G_T 9.531587e-06 4.763832e-05 -5.164134e-05
#> chr8:27131169_T_A -9.811128e-05 -1.830542e-04 3.433311e-06
#> chr8:27131173_C_T 9.253716e-05 1.367759e-04 2.367578e-04
#> chr8:27131449_G_A 7.740674e-05 6.239321e-05 -4.925159e-05
#> chr8:27131584_G_A 3.578542e-05 8.451843e-05 -1.495075e-04
#> chr8:27132152_T_C 3.644945e-05 1.570140e-04 -2.528394e-05
#> cond_4 cond_5 cond_6
#> chr8:27119632_TA_T 1.333211e-04 1.348553e-04 4.734385e-04
#> chr8:27119646_A_AG -6.910111e-05 -2.101112e-05 -1.104293e-04
#> chr8:27119646_A_G -2.529216e-05 5.465448e-05 -1.995286e-04
#> chr8:27119788_C_T -2.002414e-04 6.673100e-06 1.314975e-04
#> chr8:27119867_G_T -2.003132e-04 6.675583e-06 1.314728e-04
#> chr8:27119961_G_T 1.590978e-04 2.123016e-04 5.450551e-04
#> chr8:27120636_C_T -5.716944e-05 -6.470740e-05 -2.431535e-04
#> chr8:27120932_A_G -8.971807e-05 6.455779e-05 1.552973e-04
#> chr8:27121290_T_C -8.869541e-05 1.441139e-05 -2.548621e-04
#> chr8:27121498_C_A -8.871171e-05 1.441796e-05 -2.547996e-04
#> chr8:27121702_G_A -4.984068e-05 7.170860e-05 1.941631e-04
#> chr8:27121936_A_G -2.529681e-05 5.465705e-05 -1.994059e-04
#> chr8:27122117_CAA_C 9.633365e-05 1.053657e-04 -1.532798e-04
#> chr8:27122117_CAAA_C -2.200955e-04 -3.853014e-05 4.463472e-05
#> chr8:27122139_A_C 1.370686e-04 2.574996e-04 5.041369e-04
#> chr8:27122351_G_A -8.512209e-05 -1.300445e-05 -2.352769e-04
#> chr8:27123070_G_C -1.038997e-04 -4.387650e-05 -4.528299e-04
#> chr8:27123164_C_T -9.365608e-05 -3.714829e-05 -8.009951e-04
#> chr8:27123274_T_TG 1.854900e-04 2.644445e-04 5.342365e-04
#> chr8:27123283_T_TTTTTGTTTTGTTTTG -8.398393e-05 -1.092985e-04 -5.937819e-04
#> chr8:27123283_T_TTTTTGTTTTG -1.778457e-04 4.061584e-05 1.767367e-04
#> chr8:27123283_T_TTTTTGTTTTGTTTTGTTTTG 3.951229e-05 -1.422705e-04 -3.014142e-03
#> chr8:27123383_C_T -1.138789e-04 -5.314172e-05 -4.721660e-04
#> chr8:27123630_G_C -1.264694e-04 -5.577567e-05 -4.449484e-04
#> chr8:27123806_T_C -1.139178e-04 -5.315673e-05 -4.719245e-04
#> chr8:27124049_A_G -1.139360e-04 -5.316346e-05 -4.717986e-04
#> chr8:27124126_T_C -5.722742e-05 -6.478380e-05 -2.430545e-04
#> chr8:27124147_C_A -1.139588e-04 -5.317554e-05 -4.716639e-04
#> chr8:27124381_A_G 1.876981e-06 -1.556162e-04 -9.931371e-05
#> chr8:27124644_G_A -2.534452e-05 5.463083e-05 -1.990342e-04
#> chr8:27124683_C_T -5.725052e-05 -6.480476e-05 -2.430431e-04
#> chr8:27125591_C_G 1.875551e-06 -1.556515e-04 -9.932089e-05
#> chr8:27125730_A_G 6.736144e-05 6.774776e-05 -5.829053e-05
#> chr8:27125829_T_A 2.049563e-05 -1.574088e-04 -8.071568e-05
#> chr8:27126386_A_G -1.378124e-04 -9.942913e-05 -3.702242e-04
#> chr8:27126486_C_T -2.535353e-05 5.464137e-05 -1.989828e-04
#> chr8:27127215_T_A -7.735518e-05 -6.126329e-05 -1.077756e-04
#> chr8:27127370_T_C 1.300924e-06 -1.473641e-04 -5.850030e-06
#> chr8:27127374_T_C 1.296814e-06 -1.473966e-04 -5.861474e-06
#> chr8:27127405_T_C -2.535314e-05 5.465817e-05 -1.989349e-04
#> chr8:27128069_G_A -1.140204e-04 -5.315913e-05 -4.713806e-04
#> chr8:27128102_T_TAAAG -1.184147e-04 -4.909263e-05 -5.141105e-04
#> chr8:27128473_C_G 1.767733e-04 2.769283e-04 4.191423e-04
#> chr8:27128733_G_T -5.729842e-05 -6.484377e-05 -2.430232e-04
#> chr8:27129375_G_GA -1.140905e-04 -5.321474e-05 -4.710977e-04
#> chr8:27129602_T_C -1.199968e-04 -6.626761e-05 -5.032951e-04
#> chr8:27129674_A_G -1.141300e-04 -5.323111e-05 -4.708447e-04
#> chr8:27129849_TAAA_T 1.804257e-04 2.811869e-04 4.823381e-04
#> chr8:27129864_G_A 1.424290e-04 2.854854e-04 3.564056e-04
#> chr8:27129921_C_T 3.099902e-05 7.175046e-05 2.263813e-04
#> chr8:27130038_G_A 1.770908e-04 2.773634e-04 4.191287e-04
#> chr8:27130250_G_C -1.692897e-06 -1.659237e-04 -2.264446e-05
#> chr8:27130586_G_C -1.142258e-04 -5.333946e-05 -4.706427e-04
#> chr8:27130820_A_T -7.749873e-05 -6.138095e-05 -1.075699e-04
#> chr8:27131153_G_T -2.541236e-05 5.461350e-05 -1.987414e-04
#> chr8:27131169_T_A -1.690024e-06 -1.659619e-04 -2.268293e-05
#> chr8:27131173_C_T 1.354655e-04 3.000547e-04 3.670448e-04
#> chr8:27131449_G_A -2.147928e-04 -1.319231e-05 9.490031e-05
#> chr8:27131584_G_A -1.142940e-04 -5.337398e-05 -4.704558e-04
#> chr8:27132152_T_C -7.756371e-05 -6.141394e-05 -1.075415e-04
#> cond_7
#> chr8:27119632_TA_T -9.704702e-05
#> chr8:27119646_A_AG 1.429368e-04
#> chr8:27119646_A_G 2.879034e-04
#> chr8:27119788_C_T 1.405872e-04
#> chr8:27119867_G_T 1.406030e-04
#> chr8:27119961_G_T 2.503668e-05
#> chr8:27120636_C_T -4.317789e-04
#> chr8:27120932_A_G -7.098063e-06
#> chr8:27121290_T_C 4.083336e-04
#> chr8:27121498_C_A 4.084085e-04
#> chr8:27121702_G_A -1.328556e-04
#> chr8:27121936_A_G 2.879520e-04
#> chr8:27122117_CAA_C 2.099835e-04
#> chr8:27122117_CAAA_C 5.638159e-05
#> chr8:27122139_A_C 5.045142e-05
#> chr8:27122351_G_A 3.583430e-04
#> chr8:27123070_G_C 5.623094e-05
#> chr8:27123164_C_T -1.913291e-05
#> chr8:27123274_T_TG 5.248590e-05
#> chr8:27123283_T_TTTTTGTTTTGTTTTG 1.707420e-04
#> chr8:27123283_T_TTTTTGTTTTG 1.742456e-04
#> chr8:27123283_T_TTTTTGTTTTGTTTTGTTTTG -2.955389e-05
#> chr8:27123383_C_T 6.330575e-05
#> chr8:27123630_G_C 6.539634e-05
#> chr8:27123806_T_C 6.329283e-05
#> chr8:27124049_A_G 6.328707e-05
#> chr8:27124126_T_C -4.320143e-04
#> chr8:27124147_C_A 6.326784e-05
#> chr8:27124381_A_G 2.139878e-05
#> chr8:27124644_G_A 2.879343e-04
#> chr8:27124683_C_T -4.321161e-04
#> chr8:27125591_C_G 2.139001e-05
#> chr8:27125730_A_G 3.473118e-05
#> chr8:27125829_T_A 2.401481e-05
#> chr8:27126386_A_G -2.741196e-05
#> chr8:27126486_C_T 2.879527e-04
#> chr8:27127215_T_A 1.320914e-04
#> chr8:27127370_T_C 6.711706e-05
#> chr8:27127374_T_C 6.711051e-05
#> chr8:27127405_T_C 2.879721e-04
#> chr8:27128069_G_A 6.325768e-05
#> chr8:27128102_T_TAAAG 7.982487e-05
#> chr8:27128473_C_G 1.818387e-05
#> chr8:27128733_G_T -4.322606e-04
#> chr8:27129375_G_GA 6.320538e-05
#> chr8:27129602_T_C 5.942468e-05
#> chr8:27129674_A_G 6.319180e-05
#> chr8:27129849_TAAA_T 2.356410e-05
#> chr8:27129864_G_A 2.581809e-05
#> chr8:27129921_C_T 5.380233e-05
#> chr8:27130038_G_A 1.848457e-05
#> chr8:27130250_G_C 4.262235e-05
#> chr8:27130586_G_C 6.310877e-05
#> chr8:27130820_A_T 1.320125e-04
#> chr8:27131153_G_T 2.879287e-04
#> chr8:27131169_T_A 4.261182e-05
#> chr8:27131173_C_T 3.802855e-05
#> chr8:27131449_G_A 1.154618e-04
#> chr8:27131584_G_A 6.309798e-05
#> chr8:27132152_T_C 1.320102e-04