get.IDR: Posterior class probabilities, local, and adjusted IDRs.
In GMCM: Fast Estimation of Gaussian Mixture Copula Models

Description Usage Arguments Value Note Author(s) References Examples

Functions for computing posterior cluster probabilities (get.prob) in the general GMCM as well as local and adjusted irreproducibility discovery rates (get.IDR) in the special GMCM.

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get.IDR(x, par, threshold = 0.05, ...)

get.prob(x, theta, ...)

`x`	A `matrix` of observations where rows corresponds to features and columns to studies.
`par`	A vector of length 4 where `par[1]` is mixture proportion of the irreproducible component, `par[2]` is the mean value, `par[3]` is the standard deviation, and `par[4]` is the correlation of the reproducible component.
`threshold`	The threshold level of the IDR rate.
`...`	Arguments passed to `qgmm.marginal`.
`theta`	A list of parameters for the full model as described in `rtheta`.

get.IDR returns a list of length 5 with elements:

`idr`	A vector of the local idr values. I.e. the posterior probability that `x[i, ]` belongs to the irreproducible component.
`IDR`	A vector of the adjusted IDR values.
`l`	The number of reproducible features at the specified `threshold`.
`threshold`	The IDR threshold at which features are deemed reproducible.
`Khat`	A vector signifying whether the corresponding feature is reproducible or not.

get.prob returns a matrix where entry (i,j) is the posterior probability that the observation x[i, ] belongs to cluster j.

From GMCM version 1.1 get.IDR has been an internal function. Use get.prop or get.IDR instead. The function can still be accessed with GMCM:::get.idr. get.idr returns a vector where the i'th entry is the posterior probability that observation i is irreproducible. It is a simple wrapper for get.prob.

Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>

Li, Q., Brown, J. B. J. B., Huang, H., & Bickel, P. J. (2011). Measuring reproducibility of high-throughput experiments. The Annals of Applied Statistics, 5(3), 1752-1779. doi:10.1214/11-AOAS466

Tewari, A., Giering, M., & Raghunathan, A. (2011). Parametric Characterization of Multimodal Distributions with Non-gaussian Modes. IEEE 11th International Conference on Data Mining Workshops, 2011, 286-292. doi:10.1109/ICDMW.2011.135

set.seed(1123)

# True parameters
true.par <- c(0.9, 2, 0.7, 0.6)

# Simulation of data from the GMCM model
data <-  SimulateGMCMData(n = 1000, par = true.par, d = 2)

# Initial parameters
init.par <- c(0.5, 1, 0.5, 0.9)

# Nelder-Mead optimization
nm.par   <- fit.meta.GMCM(data$u, init.par = init.par, method = "NM")

# Get IDR values
res <- get.IDR(data$u, nm.par, threshold = 0.05)

# Plot results
plot(data$u, col = res$Khat, pch = c(3,16)[data$K])

  Nelder-Mead direct search function minimizer
function value for initial parameters = 171.783273
  Scaled convergence tolerance is 2.55977e-06
Stepsize computed as 0.219722
BUILD              5 227.072307 113.692422
EXTENSION          7 203.422655 80.536529
EXTENSION          9 171.783273 0.969765
LO-REDUCTION      11 125.403851 0.969765
EXTENSION         13 113.692422 -36.695436
EXTENSION         15 80.536529 -59.774697
REFLECTION        17 2.445024 -73.341823
LO-REDUCTION      19 0.969765 -73.341823
HI-REDUCTION      21 -36.695436 -73.341823
LO-REDUCTION      23 -44.519612 -73.341823
LO-REDUCTION      25 -59.774697 -73.341823
REFLECTION        27 -65.323185 -75.050504
REFLECTION        29 -67.858104 -75.735675
HI-REDUCTION      31 -69.377201 -75.735675
EXTENSION         33 -72.263424 -85.343583
LO-REDUCTION      35 -73.341823 -85.343583
EXTENSION         37 -75.050504 -90.646223
EXTENSION         39 -75.735675 -95.177646
HI-REDUCTION      41 -82.140512 -95.177646
LO-REDUCTION      43 -83.887908 -95.177646
HI-REDUCTION      45 -85.343583 -95.177646
REFLECTION        47 -89.413691 -96.366569
REFLECTION        49 -90.646223 -96.897874
LO-REDUCTION      51 -94.934992 -97.221745
REFLECTION        53 -95.177646 -97.685118
EXTENSION         55 -96.366569 -100.599712
HI-REDUCTION      57 -96.897874 -100.599712
REFLECTION        59 -97.221745 -100.606776
LO-REDUCTION      61 -97.685118 -100.606776
HI-REDUCTION      63 -98.649070 -100.606776
REFLECTION        65 -100.128410 -101.684845
LO-REDUCTION      67 -100.537253 -101.684845
EXTENSION         69 -100.599712 -101.993131
EXTENSION         71 -100.606776 -102.553812
HI-REDUCTION      73 -100.868522 -102.553812
LO-REDUCTION      75 -101.559228 -102.553812
HI-REDUCTION      77 -101.684845 -102.553812
LO-REDUCTION      79 -101.993131 -102.553812
EXTENSION         81 -102.018479 -102.717295
REFLECTION        83 -102.078186 -102.809142
LO-REDUCTION      85 -102.373072 -102.809142
REFLECTION        87 -102.553812 -102.982773
LO-REDUCTION      89 -102.705807 -102.982773
LO-REDUCTION      91 -102.717295 -102.982773
LO-REDUCTION      93 -102.809142 -102.982773
HI-REDUCTION      95 -102.858857 -102.982773
REFLECTION        97 -102.872474 -102.988904
REFLECTION        99 -102.914137 -103.035337
EXTENSION        101 -102.966506 -103.134041
LO-REDUCTION     103 -102.982773 -103.134041
LO-REDUCTION     105 -102.988904 -103.134041
LO-REDUCTION     107 -103.035337 -103.138305
REFLECTION       109 -103.108410 -103.175415
HI-REDUCTION     111 -103.122287 -103.175415
LO-REDUCTION     113 -103.134041 -103.175415
REFLECTION       115 -103.138305 -103.177946
EXTENSION        117 -103.145600 -103.202221
LO-REDUCTION     119 -103.165248 -103.202221
REFLECTION       121 -103.175415 -103.212280
EXTENSION        123 -103.177946 -103.233265
HI-REDUCTION     125 -103.192753 -103.233265
LO-REDUCTION     127 -103.202221 -103.233265
LO-REDUCTION     129 -103.207320 -103.233265
LO-REDUCTION     131 -103.212280 -103.233847
HI-REDUCTION     133 -103.226681 -103.233847
LO-REDUCTION     135 -103.228143 -103.233847
LO-REDUCTION     137 -103.229832 -103.233847
REFLECTION       139 -103.232052 -103.234894
REFLECTION       141 -103.233265 -103.234996
HI-REDUCTION     143 -103.233451 -103.235265
REFLECTION       145 -103.233847 -103.235912
LO-REDUCTION     147 -103.234894 -103.235912
HI-REDUCTION     149 -103.234996 -103.236298
HI-REDUCTION     151 -103.235265 -103.236298
LO-REDUCTION     153 -103.235825 -103.236298
LO-REDUCTION     155 -103.235832 -103.236298
LO-REDUCTION     157 -103.235912 -103.236298
LO-REDUCTION     159 -103.235974 -103.236298
REFLECTION       161 -103.235979 -103.236437
HI-REDUCTION     163 -103.236126 -103.236437
LO-REDUCTION     165 -103.236211 -103.236437
LO-REDUCTION     167 -103.236249 -103.236437
HI-REDUCTION     169 -103.236298 -103.236437
EXTENSION        171 -103.236342 -103.236483
REFLECTION       173 -103.236347 -103.236486
HI-REDUCTION     175 -103.236367 -103.236486
LO-REDUCTION     177 -103.236433 -103.236486
HI-REDUCTION     179 -103.236437 -103.236486
LO-REDUCTION     181 -103.236453 -103.236493
LO-REDUCTION     183 -103.236474 -103.236494
LO-REDUCTION     185 -103.236483 -103.236498
LO-REDUCTION     187 -103.236486 -103.236498
LO-REDUCTION     189 -103.236493 -103.236501
LO-REDUCTION     191 -103.236494 -103.236501
HI-REDUCTION     193 -103.236495 -103.236501
HI-REDUCTION     195 -103.236498 -103.236501
HI-REDUCTION     197 -103.236498 -103.236502
REFLECTION       199 -103.236499 -103.236503
LO-REDUCTION     201 -103.236500 -103.236503
HI-REDUCTION     203 -103.236501 -103.236503
Exiting from Nelder Mead minimizer
    205 function evaluations used