Nothing
## ---- 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`
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