## ----setup, echo=FALSE, results="hide", warning=FALSE---------------------- suppressPackageStartupMessages({ library("srnadiff") library("BiocManager") library("BiocStyle") library("knitr") library("rmarkdown") library("grid") }) knitr::opts_chunk$set( error=FALSE, fig.height=5, fig.width=8, message=FALSE, warning=FALSE, tidy=FALSE ) ## ----echo=FALSE------------------------------------------------------------ basedir <- system.file("extdata", package="srnadiff", mustWork=TRUE) sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv")) bamFiles <- paste(file.path(basedir, sampleInfo$FileName), "bam", sep=".") 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", version="3.8") ## ---- loadLibrary, eval=FALSE---------------------------------------------- # library(srnadiff) ## ---- helpSearch, eval=FALSE----------------------------------------------- # help.search("srnadiff") ## ----message=FALSE, warning=FALSE------------------------------------------ ## Determine the path to data files basedir <- system.file("extdata", package="srnadiff", mustWork=TRUE) ## Vector with the full paths to the BAM files to use bamFiles <- paste(file.path(basedir, sampleInfo$FileName), "bam", sep=".") ## Reads sample information file and creates a data frame from it sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv")) ## Vector with the full paths to the BAM files to use bamFiles <- paste(file.path(basedir, sampleInfo$FileName), "bam", sep = ".") ## 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 ## -------------------------------------------------------------------------- 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 <- paste(file.path(basedir, sampleInfo$FileName), "bam", sep=".") 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) ## ---- fig.height=3.5, fig.width=4, fig.align='center', out.width='450pt'---- plotRegions(srnaExp, regions(srnaExp)[1]) ## ---- echo=FALSE, fig.height=9--------------------------------------------- types <- list("p", "l", "b", "a", c("a", "confint"), c("a", "p", "confint")) ncols <- 2 nrows <- 3 grid.newpage() pushViewport(viewport(layout=grid.layout(nrows, ncols))) for(i in 1:length(types)){ pushViewport(viewport(layout.pos.col=((i - 1) %% ncols) + 1, layout.pos.row=(((i) - 1) %/% ncols) + 1)) trN <- paste(types[[i]], collapse=", ") plotRegions(srnaExp, regions(srnaExp)[1], type=types[[i]], trNames=c("DER", trN), chrTitle=FALSE, add=TRUE) popViewport(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) ## ---- threads, eval=FALSE-------------------------------------------------- # exp <- setNThreads(exp, nThreads=4) ## ---- session_info--------------------------------------------------------- devtools::session_info()