## ----setup_knitr, include = FALSE, cache = FALSE------------------------- library("srnadiff") library("BiocStyle") library("knitr") library("rmarkdown") opts_chunk$set(message = FALSE, error = FALSE, warning = FALSE, cache = FALSE, fig.width = 5, fig.height = 5) ## ---- standard, results="hide", warning=FALSE---------------------------- dir <- system.file("extdata", package="srnadiff", mustWork = TRUE) data <- read.csv(file.path(dir, "data.csv")) gtfFile <- file.path(dir, "Homo_sapiens.GRCh38.76.gtf.gz") annotation <- readWholeGenomeAnnotation(gtfFile) bamFiles <- file.path(dir, data$FileName) replicates <- data$SampleName conditions <- factor(data$Condition) exp <- sRNADiffExp(annotation, bamFiles, replicates, conditions) diffRegions <- runAll(exp) ## ---- example------------------------------------------------------------ exp <- sRNADiffExample() diffRegions <- runAll(exp) ## ---- read_whole_genome-------------------------------------------------- gtfFile <- file.path(dir, "Homo_sapiens.GRCh38.76.gtf.gz") annotation <- readWholeGenomeAnnotation(gtfFile) ## ---- read_mirbase_pre--------------------------------------------------- gffFile <- file.path(dir, "mirbase21_GRCh38.gff3") annotation <- readMiRBasePreAnnotation(gffFile) ## ---- read_mirbase_mature------------------------------------------------ annotation <- readMiRBaseMatureAnnotation(gffFile) ## ---- read_annotation---------------------------------------------------- annotation <- readAnnotation(gtfFile, source="miRNA", feature="gene", name="gene_name") ## ---- set_merge_distance------------------------------------------------- exp <- setMergeDistance(exp, 100) ## ---- hmm---------------------------------------------------------------- exp <- setTransitionProbabilities(exp, noDiffToDiff = 0.0001, diffToNoDiff = 0.01) exp <- setEmissionProbabilities(exp, probability = 0.9) exp <- setEmissionThreshold(exp, threshold = 0.1) ## ---- slicing------------------------------------------------------------ exp <- setMinDifferences(exp, differences = 50) ## ---- general_parameters------------------------------------------------- exp <- setMinDepth(exp, depth = 10) exp <- setSizes(exp, minSize = 15, maxSize = 1000) ## ---- strategies--------------------------------------------------------- exp <- setStrategies(exp, annotation = TRUE, naive = FALSE, hmm = TRUE, slice = TRUE) ## ---- minOverlap--------------------------------------------------------- exp <- setMinOverlap(exp, minOverlap = 20) ## ----regions------------------------------------------------------------- exp <- sRNADiffExample() exp <- runAll(exp) regions <- regions(exp, pvalue = 0.5) ## ---- plot--------------------------------------------------------------- plotRegion(exp, regions[1]) ## ---- conditions--------------------------------------------------------- conditions <- factor(c("wt", "wt", "ko", "ko"), levels=c("wt", "ko")) ## ---- threads------------------------------------------------------------ exp <- setNThreads(exp, nThreads = 4) ## ---- session_info------------------------------------------------------- devtools::session_info()