## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("ompBAM") ## ----eval=FALSE--------------------------------------------------------------- # install.packages(c("devtools", "usethis")) ## ----------------------------------------------------------------------------- library(ompBAM) pkg_path = file.path(tempdir(), "MyPkg") use_ompBAM(pkg_path) ## ----------------------------------------------------------------------------- devtools::document(pkg_path) ## ----------------------------------------------------------------------------- devtools::load_all(pkg_path) ## ----------------------------------------------------------------------------- library(MyPkg) ## ----------------------------------------------------------------------------- idxstats(ompBAM::example_BAM("Unsorted"), 2) ## ----------------------------------------------------------------------------- idxstats(ompBAM::example_BAM("scRNAseq"), 2) ## ----eval=FALSE--------------------------------------------------------------- # library(ompBAM) # project_path = "\path\to\MyPkg" # use_ompBAM(project_path) ## ----eval=FALSE--------------------------------------------------------------- # devtools::document() ## ----------------------------------------------------------------------------- library(ompBAM) pkg_path = file.path(tempdir(), "myPkgName") use_ompBAM(pkg_path) ## ----eval=FALSE--------------------------------------------------------------- # use_ompBAM("/path/to/myPkgName") ## ----eval=FALSE--------------------------------------------------------------- # #' @useDynLib myPkgName, .registration = TRUE # #' @import Rcpp # #' @import zlibbioc # NULL # # #' @export # idxstats <- function(bam_file, n_threads) { # idxstats_pbam(bam_file, n_threads) # } ## ----eval=FALSE--------------------------------------------------------------- # idxstats(ompBAM::example_BAM("Unsorted"), 2) ## ----eval=FALSE--------------------------------------------------------------- # # this is added to R/ompBAM_imports.R by use_ompBAM() # # #' @export # idxstats <- function(bam_file, n_threads) { # idxstats_pbam(bam_file, n_threads) # } ## ----eval=FALSE--------------------------------------------------------------- # source_path = system.file("examples", "ompBAMExample", "src", # package = "ompBAM") ## ----------------------------------------------------------------------------- sessionInfo()