inst/doc/famat.R

In famat: Functional analysis of metabolic and transcriptomic data

## ----style, echo = FALSE, results = 'asis'------------------------------------
BiocStyle::markdown()

## ---- eval=FALSE--------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("famat")

## ----load_famat, message=FALSE, warning=FALSE---------------------------------
library(famat)

## ----pathenrich---------------------------------------------------------------
data(genes)
data(meta)

listr=path_enrich("REAC", meta, genes)

## ----interactions-------------------------------------------------------------
data(listk)
data(listr)
data(listw)

interactions_result = interactions(listk, listr, listw)

## ----compldata, message = FALSE-----------------------------------------------
data(interactions_result)

compl_data_result <- compl_data(interactions_result)

## ---- eval=FALSE--------------------------------------------------------------
#  data(compl_data_result)
#  
#  rshiny(compl_data_result)

## ----famat, eval=FALSE--------------------------------------------------------
#  data(genes)
#  data(meta)
#  
#  listk <- path_enrich("KEGG", meta, genes)
#  listr <- path_enrich("REAC", meta, genes)
#  listw <- path_enrich("WP", meta, genes)
#  
#  interactions_result <- interactions(listk, listr, listw)
#  
#  compl_data_result <- compl_data(interactions_result)
#  
#  rshiny(compl_data_result)

## -----------------------------------------------------------------------------
sessionInfo()