## ----setup, echo=FALSE, results="hide", warning=FALSE------------------------- suppressPackageStartupMessages({ library("srnadiff") library("BiocManager") library("BiocStyle") library("knitr") library("rmarkdown") library("grid") }) knitr::opts_chunk$set( error=FALSE, fig.height=5, fig.width=8, message=FALSE, warning=FALSE, tidy=FALSE ) ## ----echo=FALSE--------------------------------------------------------------- basedir <- system.file("extdata", package="srnadiff", mustWork=TRUE) sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv")) bamFiles <- file.path(basedir, sampleInfo$FileName) gtfFile <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz") annotReg <- readAnnotation(gtfFile, feature="gene", source="miRNA") ## ----eval=TRUE, echo=FALSE---------------------------------------------------- x <- citation("srnadiff") ## ----eval=FALSE, message=FALSE, warning=FALSE--------------------------------- # help("srnadiff") ## ----eval=FALSE, message=FALSE, warning=FALSE--------------------------------- # ?srnadiff ## ----message=FALSE, warning=FALSE, include=FALSE, results="hide"-------------- #-- Data preparation srnaExp <- srnadiffExp(bamFiles, sampleInfo) #-- Performing srnadiff srnaExp <- srnadiff(srnaExp) #-- Visualization of the results plotRegions(srnaExp, regions(srnaExp)[1]) ## ---- bioconductor, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") ## ---- install, eval=FALSE----------------------------------------------------- # BiocManager::install("srnadiff") ## ---- loadLibrary, eval=FALSE------------------------------------------------- # library(srnadiff) ## ---- helpSearch, eval=FALSE-------------------------------------------------- # help.search("srnadiff") ## ----message=FALSE, warning=FALSE--------------------------------------------- ## Specifiy path to data files basedir <- system.file("extdata", package="srnadiff", mustWork=TRUE) ## Read sample information file, and create a data frame sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv")) ## Vector with the full paths to the BAM files to use bamFiles <- file.path(basedir, sampleInfo$FileName) ## Creates an srnadiffExp object srnaExp <- srnadiffExp(bamFiles, sampleInfo) ## ---- eval=FALSE-------------------------------------------------------------- # srnaExp <- srnadiffExp(bamFiles, sampleInfo, annotReg) ## ----message=FALSE, warning=FALSE--------------------------------------------- srnaExp <- srnadiffExp(bamFiles, sampleInfo) annotReg(srnaExp) <- annotReg ## ----message=FALSE, warning=FALSE--------------------------------------------- sampleInfo$Condition <- factor(sampleInfo$Condition, levels = c("control", "infected")) ## ----------------------------------------------------------------------------- srnaExp ## ----------------------------------------------------------------------------- srnaExp <- srnadiffExample() ## ----message=FALSE, warning=FALSE--------------------------------------------- basedir <- system.file("extdata", package="srnadiff", mustWork=TRUE) sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv")) gtfFile <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz") annotReg <- readAnnotation(gtfFile, feature="gene", source="miRNA") bamFiles <- file.path(basedir, sampleInfo$FileName) srnaExp <- srnadiffExp(bamFiles, sampleInfo, annotReg) ## ----message=FALSE, warning=FALSE--------------------------------------------- gtfFile <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz") annotReg <- readAnnotation(gtfFile, feature="gene", source="miRNA") ## ----message=FALSE, warning=FALSE--------------------------------------------- gffFile <- file.path(basedir, "mirbase21_GRCh38.gff3") annotReg <- readAnnotation(gffFile, feature="miRNA_primary_transcript") ## ----message=FALSE, warning=FALSE--------------------------------------------- gffFile <- file.path(basedir, "mirbase21_GRCh38.gff3") annotReg <- readAnnotation(gffFile, feature="miRNA") ## ----message=FALSE, warning=FALSE--------------------------------------------- annotation <- readAnnotation(gtfFile, source="miRNA", feature="gene") ## ----------------------------------------------------------------------------- srnaExp <- srnadiff(srnaExp) ## ----------------------------------------------------------------------------- sampleInfo(srnaExp) ## ----------------------------------------------------------------------------- chromosomeSizes(srnaExp) ## ----------------------------------------------------------------------------- parameters(srnaExp) ## ----message=FALSE, warning=FALSE--------------------------------------------- regions <- regions(srnaExp, pvalue=0.5) ## ----message=FALSE, warning=FALSE--------------------------------------------- library(rtracklayer) export(regions, "file.bed") ## ---- fig.height=3.5, fig.width=4, fig.align='center', out.width='450pt'------ plotRegions(srnaExp, regions(srnaExp)[1]) ## ---- eval=FALSE-------------------------------------------------------------- # parameters(srnaExp) <- list(noDiffToDiff=0.01, emissionThreshold=0.2) ## ---- eval=FALSE-------------------------------------------------------------- # parameters(srnaExp) <- list(minLogFC=1) ## ---- eval=FALSE-------------------------------------------------------------- # parameters(srnaExp) <- list(cutoff=1.5) ## ---- general_parameter------------------------------------------------------- parameters(srnaExp) <- list(minDepth=1) parameters(srnaExp) <- list(minSize=15, maxSize=1000) ## ---- strategies-------------------------------------------------------------- srnaExp <- srnadiffExample() srnaExp <- srnadiff(srnaExp, segMethod=c("hmm", "IR")) ## ---- minOverlap-------------------------------------------------------------- parameters(srnaExp) <- list(minOverlap=1000) ## ---- pvalue_edger------------------------------------------------------------ srnaExp <- srnadiffExample() srnaExp <- srnadiff(srnaExp, diffMethod="edgeR") ## ---- pvalue_bayseq----------------------------------------------------------- srnaExp <- srnadiffExample() srnaExp <- srnadiff(srnaExp, diffMethod="baySeq") ## ---- threads, eval=FALSE----------------------------------------------------- # exp <- setNThreads(exp, nThreads=4) ## ---- session_info------------------------------------------------------------ devtools::session_info()