## ----warning=FALSE, error=F--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=F, echo=T----------------------------------------------------------- # # install.packages("BiocManager") # BiocManager::install("uncoverappLib") # library(uncoverappLib) ## ----eval=F, echo=T----------------------------------------------------------- # # #library(devtools) # #install_github("Manuelaio/uncoverappLib") # #library(uncoverappLib) # ## ----eval=TRUE, echo=TRUE----------------------------------------------------- library(uncoverappLib) #getAnnotationFiles(verbose= TRUE, vignette= TRUE) ## ----eval=TRUE, echo=TRUE----------------------------------------------------- gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib") ## ----eval=TRUE, echo=TRUE----------------------------------------------------- bam_example <- system.file("extdata", "example_POLG.bam", package = "uncoverappLib") print(bam_example) write.table(bam_example, file= "./bam.list", quote= FALSE, row.names = FALSE, col.names = FALSE) ## ----echo = FALSE, out.width='80%', fig.align='center', fig.cap="Screenshot of Preprocessing page."---- knitr::include_graphics("pre_file.png") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # chr15 89859516 89859516 68 A:68 # chr15 89859517 89859517 70 T:70 # chr15 89859518 89859518 73 A:2;G:71 # chr15 89859519 89859519 73 A:73 # chr15 89859520 89859520 74 C:74 # chr15 89859521 89859521 75 C:1;T:74 # ## ----echo = FALSE, out.width='100%', fig.align='center', fig.cap="Screenshot of Coverage Analysis page."---- knitr::include_graphics("load_file.png") ## ----echo = FALSE, out.width='100%', fig.align='center', fig.cap="Screenshot of output of UCSC gene table."---- knitr::include_graphics("ucsc_info.png") ## ----echo = FALSE, out.width='100%', fig.align='center', fig.cap="Screenshot of output of Exon genomic coordinate positions from UCSC table."---- knitr::include_graphics("exon_info.png") ## ----echo = FALSE, out.width='100%', fig.align='center', fig.cap="Screenshot of output of gene coverage."---- knitr::include_graphics("all_gene.png") ## ----echo = FALSE, out.width='80%', fig.align='center', fig.cap= "zoom of exon 10 "---- knitr::include_graphics("exon10tab.png") ## ----echo = FALSE, out.width='80%', fig.align='center', fig.cap=" Example of uncovered positions annotate with dbNSFP."---- knitr::include_graphics("annotate.png") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()