## ----setup, include = FALSE--------------------------------------------------- library(DegNorm) knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(knitr) knit_hooks$set(optipng = hook_optipng) ## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("DegNorm") ## ----------------------------------------------------------------------------- ## specify bam_files from RNA-seq, you should replace it by your own bam files bam_file_list=list.files(path=system.file("extdata",package="DegNorm"), pattern=".bam$",full.names=TRUE) ## ----------------------------------------------------------------------------- ## gtf_file you used for RNA-seq alignment, replace it by your own gtf file gtf_file=list.files(path=system.file("extdata",package="DegNorm"), pattern=".gtf$",full.names=TRUE) ## ----eval=TRUE---------------------------------------------------------------- ## calculate the read coverage score for all genes of all samples coverage_res_chr21_sub=read_coverage_batch(bam_file_list, gtf_file,cores=2) ## ----eval=FALSE--------------------------------------------------------------- # ## save the coverage results # save(coverage_res_chr21_sub,file="coverage_res_chr21_sub.Rda") ## ----------------------------------------------------------------------------- data("coverage_res_chr21") ## summarize the coverage results summary_CoverageClass(coverage_res_chr21) ## ----------------------------------------------------------------------------- ## extract coverage scores and counts from coverage_res coverage_matrix=coverage_res_chr21$coverage counts=coverage_res_chr21$counts ## ----eval=TRUE---------------------------------------------------------------- res_DegNorm_chr21 = degnorm(read_coverage = coverage_res_chr21[[1]], counts = coverage_res_chr21[[2]], iteration = 5, down_sampling = 1, grid_size=10, loop = 100, cores=2) ## ----eval=FALSE--------------------------------------------------------------- # ## save the DegNorm results # save(res_DegNorm_chr21,file="res_DegNorm_chr21.Rda") ## ----------------------------------------------------------------------------- data("res_DegNorm_chr21") ## ----------------------------------------------------------------------------- ## summary of the DegNorm output summary_DegNormClass(res_DegNorm_chr21) ## ----------------------------------------------------------------------------- ## extrac normalized read counts counts_normed=res_DegNorm_chr21$counts_normed ## ----fig.width=5,fig.height=4,message=FALSE,eval=TRUE------------------------- ##gene named "SOD1" plot_coverage(gene_name="SOD1", coverage_output=coverage_res_chr21, degnorm_output=res_DegNorm_chr21,group=c(0,1,1)) ## ----fig.width=5,fig.height=4,message=FALSE,eval=TRUE------------------------- ##gene named "SOD1" plot_coverage(gene_name="SOD1", coverage_output=coverage_res_chr21, degnorm_output=res_DegNorm_chr21,group=c(0,1), samples=c("SRR873822_chr21.bam", "SRR873834_chr21.bam")) ## ----fig.width=5,fig.height=4,message=FALSE,warning=FALSE,eval=TRUE----------- plot_boxplot(DI=res_DegNorm_chr21$DI) ## ----fig.width=5,fig.height=4,message=FALSE,eval=TRUE------------------------- plot_heatmap(DI=res_DegNorm_chr21$DI) ## ----fig.width=5,fig.height=4,message=FALSE,warning=FALSE,eval=TRUE----------- plot_corr(DI=res_DegNorm_chr21$DI) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()