## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- library(RiboCrypt) # This package library(ORFik) # The backend package for RiboCrypt ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- df <- ORFik.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-------------------------------- dir <- system.file("extdata/Homo_sapiens_sample", "", package = "ORFik") # 2. Pick an experiment name exper <- "ORFik_tutorial_data" # 3. Pick .gff/.gtf location txdb <- system.file("extdata/Homo_sapiens_sample", "Homo_sapiens_dummy.gtf.db", package = "ORFik") fa <- system.file("extdata/Homo_sapiens_sample", "Homo_sapiens_dummy.fasta", package = "ORFik") all_experiments_dir <- ORFik::config()["exp"] # <- Here they are template <- create.experiment(dir = dir, saveDir = all_experiments_dir, exper, txdb = txdb, fa = fa, organism = "Homo sapiens simulated", author = "Simulated by ORFik", types = "ofst") ## ----eval = TRUE, echo = TRUE, message = FALSE-------------------------------- convert_to_bigWig(df) ## ----eval = FALSE, echo = TRUE, message = FALSE------------------------------- # # Just set some settings for this tutorial to look cool, usually you can ignore these # browser_options <- c(default_frame_type = "columns", default_experiment = "ORFik_tutorial_data", default_libs = paste0(c("CAGE_WT_r1", "PAS_WT_r1", "RFP_WT_r1", "RNA_WT_r1"), collapse = "|"), plot_on_start = TRUE) # # RiboCrypt_app(browser_options = browser_options) ## ----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)