## ----para, echo = FALSE, results='hide'--------------------------------------- knitr::opts_chunk$set(dev="png",fig.show="hold", fig.width=8,fig.height=4.5,fig.align="center", message=FALSE,collapse=TRUE) ## ---- eval=FALSE-------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("exomePeak2") ## ---- eval = TRUE------------------------------------------------------------- library(exomePeak2) set.seed(1) GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2") f1 = system.file("extdata", "IP1.bam", package="exomePeak2") f2 = system.file("extdata", "IP2.bam", package="exomePeak2") f3 = system.file("extdata", "IP3.bam", package="exomePeak2") f4 = system.file("extdata", "IP4.bam", package="exomePeak2") IP_BAM = c(f1,f2,f3,f4) f1 = system.file("extdata", "Input1.bam", package="exomePeak2") f2 = system.file("extdata", "Input2.bam", package="exomePeak2") f3 = system.file("extdata", "Input3.bam", package="exomePeak2") INPUT_BAM = c(f1,f2,f3) exomePeak2(bam_ip = IP_BAM, bam_input = INPUT_BAM, gff_dir = GENE_ANNO_GTF, genome = "hg19", paired_end = FALSE) ## ---- eval = TRUE------------------------------------------------------------- f1 = system.file("extdata", "treated_IP1.bam", package="exomePeak2") TREATED_IP_BAM = c(f1) f1 = system.file("extdata", "treated_Input1.bam", package="exomePeak2") TREATED_INPUT_BAM = c(f1) exomePeak2(bam_ip = IP_BAM, bam_input = INPUT_BAM, bam_treated_input = TREATED_INPUT_BAM, bam_treated_ip = TREATED_IP_BAM, gff_dir = GENE_ANNO_GTF, genome = "hg19", paired_end = FALSE) ## ---- eval = TRUE------------------------------------------------------------- f2 = system.file("extdata", "mod_annot.rds", package="exomePeak2") MOD_ANNO_GRANGE <- readRDS(f2) exomePeak2(bam_ip = IP_BAM, bam_input = INPUT_BAM, gff_dir = GENE_ANNO_GTF, genome = "hg19", paired_end = FALSE, mod_annot = MOD_ANNO_GRANGE) ## ---- eval = TRUE------------------------------------------------------------- MeRIP_Seq_Alignment <- scanMeripBAM( bam_ip = IP_BAM, bam_input = INPUT_BAM, paired_end = FALSE ) ## ---- eval = TRUE------------------------------------------------------------- MeRIP_Seq_Alignment <- scanMeripBAM( bam_ip = IP_BAM, bam_input = INPUT_BAM, bam_treated_input = TREATED_INPUT_BAM, bam_treated_ip = TREATED_IP_BAM, paired_end = FALSE ) ## ---- eval = TRUE------------------------------------------------------------- SummarizedExomePeaks <- exomePeakCalling(merip_bams = MeRIP_Seq_Alignment, gff_dir = GENE_ANNO_GTF, genome = "hg19") ## ---- eval = TRUE------------------------------------------------------------- SummarizedExomePeaks <- exomePeakCalling(merip_bams = MeRIP_Seq_Alignment, gff_dir = GENE_ANNO_GTF, genome = "hg19", mod_annot = MOD_ANNO_GRANGE) ## ---- eval = TRUE------------------------------------------------------------- SummarizedExomePeaks <- estimateSeqDepth(SummarizedExomePeaks) SummarizedExomePeaks <- normalizeGC(SummarizedExomePeaks) ## ---- eval = FALSE------------------------------------------------------------ # SummarizedExomePeaks <- glmM(SummarizedExomePeaks) ## ---- eval = TRUE, warning=FALSE---------------------------------------------- SummarizedExomePeaks <- glmDM(SummarizedExomePeaks) ## ---- eval = TRUE, fig.align='center', fig.height = 2.8, fig.width = 5-------- plotLfcGC(SummarizedExomePeaks, point_size = 1, xlim = c(0.4, 0.85)) ## ---- eval = TRUE------------------------------------------------------------- plotSizeFactors(SummarizedExomePeaks) ## ---- eval = TRUE, fig.width=10, fig.height=7--------------------------------- exportResults(SummarizedExomePeaks, format = "BED") ## ----------------------------------------------------------------------------- sessionInfo()