# Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

#### Nathalie Villa-Vialaneix

# Introduction

The R package `RNAseqNet` can be used to infer networks from RNA-seq expression data. The count data are given as a \(n \times p\) matrix in which \(n\) is the number of individuals and \(p\) the number of genes. This matrix is denoted by \(\mathbf{X}\) in the sequel.

Eventually, the RNA-seq dataset is complemented with an \(n' \times d\) matrix, \(\mathbf{Y}\) which can be used to impute missing individuals in \(\mathbf{X}\) as described in [Imbert et al., 2018]1.

# Dataset description

Two datasets are available in the package: `lung` and `thyroid` with \(n = 221\) rows and respectively 100 and 50 columns. The raw data were downloaded from https://gtexportal.org/. The TMM normalisation of RNA-seq expression was performed with the R package `edgeR`.

Data are loaded with:

    data(lung)
    boxplot(log2(lung + 1), las = 3, cex.names = 0.5)

    data(thyroid)
    boxplot(log2(thyroid + 1), las = 3, cex.names = 0.5)

# Network inference from RNA-seq data

Network inference from RNA-seq data is performed with the Poisson GLM model described in [Allen and Liu, 2012]2. The inference can be performed with the function `GLMnetwork` as follows:

    lambdas <- 4 * 10^(seq(0, -2, length = 10))
    ref_lung <- GLMnetwork(lung, lambdas = lambdas)

The entry `path` of `ref_lung` contains `length(lambdas)` = 10 matrices with estimated coefficients. Each matrix is a square matrix with `ncol(lung)` = 100 rows and columns.

The choice of the most appropriate value for \(\lambda\) can be performed with the StARS criterion of [Liu et al., 2010]3, which is implemented in the function `stabilitySelection`. The argument `B` is used to specify the number of re-sampling used to compute the stability criterion:

    set.seed(11051608)
    stability_lung <- stabilitySelection(lung, lambdas = lambdas, B = 50)
    plot(stability_lung)

The entry `best` of `stability_lung` is the index of the chosen \(\lambda\) in `lambdas`. Here, the value \(\lambda=\) `lambdas[stability_lung$best]` = 0.3097055 is chosen.

The corresponding set of estimated coefficients, is in `ref_lung$path[[stability_lung$best]]` and can be transformed into a network with the function `GLMnetToGraph`:

    lung_refnet <- GLMnetToGraph(ref_lung$path[[stability_lung$best]])
    print(lung_refnet)

    ## IGRAPH dcc3d30 UN-- 100 454 --
    ## + attr: name (v/c)
    ## + edges from dcc3d30 (vertex names):
    ##  [1] MT-CO1--MT-ND4       MT-CO1--SFTPA2       MT-CO1--hsa-mir-6723
    ##  [4] MT-CO1--A2M          MT-CO1--MT-CO2       MT-CO1--MT-CO3
    ##  [7] MT-CO1--MT-RNR2      MT-CO1--MT-ATP6      MT-CO1--MT-ND1
    ## [10] MT-CO1--MTND2P28     MT-CO1--MT-ND6       MT-CO1--SAT1
    ## [13] MT-CO1--HSPB1        MT-CO1--MTND4P12     MT-CO1--HLA-DRA
    ## [16] MT-CO1--MTND1P23     SFTPB --SFTPA2       SFTPB --FN1
    ## [19] SFTPB --B2M          SFTPB --NEAT1        SFTPB --SLC34A2
    ## [22] SFTPB --PGC          SFTPB --CTSD         SFTPB --TSC22D3
    ## + ... omitted several edges

    set.seed(1243)
    plot(lung_refnet, vertex.size = 5, vertex.color = "orange",
         vertex.frame.color = "orange", vertex.label.cex = 0.5,
         vertex.label.color = "black")

# Network inference with an auxiliary dataset

In this section, we artificially remove some of the observations in `lung` to create missing individuals (as compared to those in `thyroid`):

    set.seed(1717)
    nobs <- nrow(lung)
    miss_ind <- sample(1:nobs, round(0.2 * nobs), replace = FALSE)
    lung[miss_ind, ] <- NA
    lung <- na.omit(lung)
    boxplot(log2(lung + 1), las = 3, cex.names = 0.5)

The method described in [Imbert et al., 2018] is thus used to infer a network for `lung` expression data, imputing missing individuals from the information provided between gene expressions by the `thyroid` dataset.

The first step of the method is to choose a relevant value for the donor list parameter, \(\sigma\). This is done computing \(V_{\textrm{intra}}\), the intra-variability in donor pool, for various values of \(\sigma\). An elbow rule is thus used to choose an appropriate value:

    sigmalist <- 1:5
    sigma_stats <- chooseSigma(lung, thyroid, sigmalist)
    p <- ggplot(sigma_stats, aes(x = sigma, y = varintra)) + geom_point() +
      geom_line() + theme_bw() +
      ggtitle(expression("Evolution of intra-pool homogeneity versus" ~ sigma)) +
      xlab(expression(sigma)) + ylab(expression(V[intra])) +
      theme(title = element_text(size = 10))
    print(p)

Here, \(\sigma = 2\) is chosen. Finally, hd-MI is processed with the chosen \(\sigma\), a list of regularization parameters \(\lambda\) that are selected with with the StARS criterion (from `B = 10` subsamples) in `m = 100` replicates of the inference, all performed on a different imputed dataset. The function `imputedGLMnetwork` is the one implementing the full method. The distribution of edge frequency among the `m = 100` inferred network is obtained with the function `plot` applied to the result of this function.

    set.seed(16051244)
    lung_hdmi <- imputedGLMnetwork(lung, thyroid, sigma = 2, lambdas = lambdas,
                                   m = 100, B = 10)
    plot(lung_hdmi)

Finally, the final graph is extracted using the function `GLMnetToGraph` on the result of the function ``imputedGLMnetwork``` and providing a threshold for edge frequency prediction.

    lung_net <- GLMnetToGraph(lung_hdmi, threshold = 0.9)
    lung_net

    ## IGRAPH ded1a65 UN-- 100 132 --
    ## + attr: name (v/c)
    ## + edges from ded1a65 (vertex names):
    ##  [1] MT-CO1      --MT-ND4        MT-CO1      --MT-CO2
    ##  [3] MT-CO1      --MT-CO3        MT-CO1      --MT-ND1
    ##  [5] SFTPB       --SLC34A2       SFTPB       --PGC
    ##  [7] SFTPB       --NAPSA         SFTPB       --ABCA3
    ##  [9] SFTPC       --SFTPA2        SFTPC       --SFTPA1
    ## [11] MT-ND4      --MT-ND4L       SFTPA2      --SFTPA1
    ## [13] hsa-mir-6723--MT-RNR2       hsa-mir-6723--MTATP6P1
    ## [15] hsa-mir-6723--RP5-857K21.11 hsa-mir-6723--MTND1P23
    ## + ... omitted several edges

    set.seed(1605)
    plot(lung_net, vertex.size = 5, vertex.color = "orange",
         vertex.frame.color = "orange", vertex.label.cex = 0.5,
         vertex.label.color = "black")

# Session information

Here is the output of `sessionInfo()` on the system on which this document was compiled:

    ## R version 3.4.3 (2017-11-30)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 16.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS: /usr/lib/libblas/libblas.so.3.6.0
    ## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] RNAseqNet_0.1.1 ggplot2_2.2.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] Rcpp_0.12.13     compiler_3.4.3   plyr_1.8.4       iterators_1.0.8
    ##  [5] tools_3.4.3      rpart_4.1-11     digest_0.6.12    evaluate_0.10.1
    ##  [9] tibble_1.3.4     gtable_0.2.0     lattice_0.20-35  pkgconfig_2.0.1
    ## [13] rlang_0.1.4      Matrix_1.2-12    foreach_1.4.3    igraph_1.1.2
    ## [17] yaml_2.1.14      stringr_1.2.0    knitr_1.17       rprojroot_1.2
    ## [21] glmnet_2.0-13    grid_3.4.3       nnet_7.3-12      mice_2.46.0
    ## [25] PoiClaClu_1.0.2  hot.deck_1.1     survival_2.41-3  rmarkdown_1.7
    ## [29] magrittr_1.5     backports_1.1.1  scales_0.5.0     codetools_0.2-15
    ## [33] htmltools_0.3.6  MASS_7.3-48      splines_3.4.3    colorspace_1.3-2
    ## [37] labeling_0.3     stringi_1.1.5    lazyeval_0.2.1   munsell_0.4.3

1. Imbert, A., Valsesia, A., Le Gall, C., Armenise, C., Lefebvre, G., Gourraud, P.A., Viguerie, N. and Villa-Vialaneix, N. (2018) Multiple hot-deck imputation for network inference from RNA sequencing data. Bioinformatics. DOI: http://dx.doi.org/10.1093/bioinformatics/btx819↩

2. Allen, G. and Liu, Z. (2012) A log-linear model for inferring genetic networks from high-throughput sequencing data. In Proceedings of IEEE International Conference on Bioinformatics and Biomedecine (BIBM)↩

3. Liu, H., Roeber, K. and Wasserman, L. (2010) Stability approach to regularization selection (StARS) for high dimensional graphical models. In Proceedings of Neural Information Processing Systems (NIPS 2010), 23, 1432-1440, Vancouver, Canada.↩