## ----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`