## ---- 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")

## ---- eval=FALSE--------------------------------------------------------------
#  library(psichomics)
#  data <- loadLocalFiles("/path/to/psichomics/input")
#  names(data)
#  names(data[[1]])
#  
#  junctionQuant  <- data[[1]]$`Junction quantification`
#  sampleInfo     <- data[[1]]$`Sample metadata`
#  # Both gene read counts and cRPKMs are loaded as separate data frames
#  geneReadCounts <- data[[1]]$`Gene expression (read counts)`
#  cRPKM          <- data[[1]]$`Gene expression (cRPKM)`

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

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

