## ----setup, echo=FALSE-------------------------------------------------------- library(knitr) options(width=80) knitr::opts_chunk$set( collapse=TRUE, comment="") ## ---- message=FALSE, warning=FALSE-------------------------------------------- library(atena) library(GenomicRanges) rmsk <- annotaTEs(genome = "dm6", parsefun = rmskbasicparser) rmsk ## ----------------------------------------------------------------------------- bamfiles <- list.files(system.file("extdata", package="atena"), pattern="*.bam", full.names=TRUE) TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds", package="atena")) empar <- ERVmapParam(bamfiles, teFeatures = TE_annot, singleEnd = TRUE, ignoreStrand = TRUE, suboptimalAlignmentCutoff=NA) empar ## ----------------------------------------------------------------------------- bamfiles <- list.files(system.file("extdata", package="atena"), pattern="*.bam", full.names=TRUE) TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds", package="atena")) gene_annot <- readRDS(file = system.file("extdata", "Top50genes.rds", package="atena")) tspar <- TelescopeParam(bfl=bamfiles, teFeatures=TE_annot, geneFeatures = gene_annot, singleEnd = TRUE, ignoreStrand=TRUE) tspar ## ----------------------------------------------------------------------------- bamfiles <- list.files(system.file("extdata", package="atena"), pattern="*.bam", full.names=TRUE) TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds", package="atena")) ttpar <- TEtranscriptsParam(bamfiles, teFeatures = TE_annot, singleEnd = TRUE, ignoreStrand=TRUE, aggregateby = c("repName")) ttpar ## ----------------------------------------------------------------------------- # Creating an example of gene annotations annot_gen <- GRanges(seqnames = rep("2L",10), ranges = IRanges(start = c(1,20,45,80,110,130,150,170,200,220), width = c(10,20,35,10,5,15,10,25,5,20)), strand = "*", type = rep("exon",10)) # Setting gene ids names(annot_gen) <- paste0("gene",c(rep(1,3),rep(2,4),rep(3,3))) annot_gen ttpar_gen <- TEtranscriptsParam(bamfiles, teFeatures = TE_annot, geneFeatures = annot_gen, singleEnd = TRUE, ignoreStrand=TRUE) ttpar_gen ## ----------------------------------------------------------------------------- features(ttpar_gen)[!attributes(features(ttpar_gen))$isTE$isTE] ## ---- results='hide'---------------------------------------------------------- emq <- qtex(empar) ## ----------------------------------------------------------------------------- emq colSums(assay(emq)) ## ---- results='hide'---------------------------------------------------------- tsq <- qtex(tspar) ## ----------------------------------------------------------------------------- tsq colSums(assay(tsq)) ## ---- results='hide'---------------------------------------------------------- ttq <- qtex(ttpar) ## ----------------------------------------------------------------------------- ttq colSums(assay(ttq)) ## ----------------------------------------------------------------------------- nrow(ttq) ## ----session_info, cache=FALSE------------------------------------------------ sessionInfo()