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

Abstract

Short vignette pointing to RNAseqNet User’s Guide.

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 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## 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-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## 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_0.6.39     desc_1.4.3        R6_2.6.1          fastmap_1.2.0    
##  [5] xfun_0.55         cachem_1.1.0      knitr_1.51        htmltools_0.5.9  
##  [9] rmarkdown_2.30    lifecycle_1.0.5   cli_3.6.5         sass_0.4.10      
## [13] pkgdown_2.2.0     textshaping_1.0.4 jquerylib_0.1.4   systemfonts_1.3.1
## [17] compiler_4.5.2    tools_4.5.2       ragg_1.5.0        bslib_0.9.0      
## [21] evaluate_1.0.5    yaml_2.3.12       otel_0.2.0        jsonlite_2.0.0   
## [25] rlang_1.1.6       fs_1.6.6          htmlwidgets_1.6.4

Nathalie Vialaneix

Alyssa Imbert

Description

Reference

Session information for the vignette