## ---- eval=FALSE--------------------------------------------------------------
#  # Change working directory to where the STAR output is
#  setwd("/path/to/aligned/output/")
#  
#  library(psichomics)
#  prepareGeneQuant(
#      "SRR6368612ReadsPerGene.out.tab", "SRR6368613ReadsPerGene.out.tab",
#      "SRR6368614ReadsPerGene.out.tab", "SRR6368615ReadsPerGene.out.tab",
#      "SRR6368616ReadsPerGene.out.tab", "SRR6368617ReadsPerGene.out.tab")
#  prepareJunctionQuant("SRR6368612SJ.out.tab", "SRR6368613SJ.out.tab",
#                       "SRR6368614SJ.out.tab", "SRR6368615SJ.out.tab",
#                       "SRR6368616SJ.out.tab", "SRR6368617SJ.out.tab")
#  prepareSRAmetadata("SraRunTable.txt")

## ---- eval=FALSE--------------------------------------------------------------
#  library(psichomics)
#  psichomics()

## ---- eval=FALSE--------------------------------------------------------------
#  library(psichomics)
#  data          <- loadLocalFiles("/path/to/aligned/output/")
#  geneExpr      <- data[[1]]$`Gene expression`
#  junctionQuant <- data[[1]]$`Junction quantification`
#  sampleInfo    <- data[[1]]$`Sample metadata`

