# 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
## [13] evaluate_0.14