## ---- 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`