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

#### Nathalie Vialaneix

# Description

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].

The RNAseqNet User’s Guide can be opened with:

    RNAseqNetUsersGuide()

The location of the source file is given by:

    RNAseqNetUsersGuide(html = FALSE)

# Reference

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.

# Session information for the vignette

    sessionInfo()

    ## R version 4.3.2 (2023-10-31)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 22.04.4 LTS
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    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
    ##
    ## locale:
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    ##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=C
    ##  [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
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    ## time zone: Europe/Paris
    ## tzcode source: system (glibc)
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    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] digest_0.6.31   R6_2.5.1        fastmap_1.1.1   xfun_0.39
    ##  [5] cachem_1.0.8    knitr_1.42      htmltools_0.5.5 rmarkdown_2.21
    ##  [9] cli_3.6.1       sass_0.4.6      jquerylib_0.1.4 compiler_4.3.2
    ## [13] rstudioapi_0.14 tools_4.3.2     evaluate_0.21   bslib_0.4.2
    ## [17] yaml_2.3.7      rlang_1.1.1     jsonlite_1.8.4