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 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] compiler_3.6.3  magrittr_1.5    htmltools_0.3.6 tools_3.6.3    
##  [5] yaml_2.2.0      Rcpp_1.0.1      stringi_1.4.3   rmarkdown_1.14 
##  [9] knitr_1.23      stringr_1.4.0   digest_0.6.20   xfun_0.8       
## [13] evaluate_0.14