## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- library(RiboCrypt) # This package library(ORFik) # The backend package for RiboCrypt ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- df <- RiboCrypt.template.experiment() cds <- loadRegion(df, "cds") cds # gene annotation df # let's look at libraries the experiment contains ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- df[4:6,] df[which(df$libtype == "CAGE"),] df[which(df$condition == "Mutant"),] ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[3], 30), 30), annotation = cds,df = df[c(1,5,9,13),], frames_type = "columns", custom_motif = "CTG") ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[3], 30), 30), annotation = cds,df = df[which(df$libtype == "RFP")[1],], frames_type = "lines") ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[3], 30), 30), annotation = cds,df = df[which(df$libtype == "RFP")[1],], frames_type = "lines", kmers = 6) ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[3], 30), 30), annotation = cds,df = df[which(df$libtype == "RFP")[1],], frames_type = "stacks", kmers = 6)