inst/doc/scTensor_4_Reanalysis.R

In scTensor: Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

## ----reanalysis.RData, eval=FALSE---------------------------------------------
#  suppressPackageStartupMessages(library("scTensor"))
#  load("reanalysis.RData")

## ----Reanalysis, eval=FALSE---------------------------------------------------
#  if(!require(LRBase.Hsa.eg.db)){
#      BiocManager::install("LRBase.Hsa.eg.db")
#      suppressPackageStartupMessages(library(LRBase.Hsa.eg.db))
#  }
#  # Register the file pass of user's LRBase
#  metadata(sce)$lrbase <- dbfile(LRBase.Hsa.eg.db)
#  # CCI Tensor Decomposition
#  cellCellDecomp(sce, ranks=c(6,5), assayNames="normcounts")
#  # HTML Report
#  cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts",
#      title="Cell-cell interaction within Germline_Male, GSE86146",
#      author="Koki Tsuyuzaki", html.open=TRUE,
#      goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE,
#      doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE)

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()