makeRegions: Utility Tools to Create and Manipulate Genomic Regions

The package “makeRegions” currently helps with the creation of genomic regions from GTF or BED files with options to filter specific features.

Installation

You can install the development version of makeRegions from GitHub with: (If cannot use any packages for installing from GitHub, see below)

# install.packages("pak")
pak::pak("tolgatabanli/makeRegions")

or

# install.packages("devtools")
devtools::install_github("tolgatabanli/makeRegions")

If you need an alternative to use this package as a user- or directory-specific library (e.g. for a remote cluster) without devtools' install_github, pak or similar:

For Linux:

1. Clone the repository locally (where you manage the packages on your own).
2. In RStudio, make sure you are at the repository root.
3. Use devtools:build(). This will generate a tar.gz file.
4. Scp the tar.gz to the remote server.
5. Use install.packages("PACKAGENAME.tar.gz", repo = NULL, lib="YOUR_LOCAL_LIB")
6. Whenever you need to attach the package, use library("PACKAGENAME", lib.loc="path/to/YOUR_LOCAL_LIB").

Example

library(makeRegions)

example_file <- system.file("extdata", "data", "example.gtf", package = "makeRegions")
result <- make_windows(input_file=example_file,
                       upstream = 1000, downstream = 2000,
                       feature = "gene", biotype = "lncRNA",
                       position = "start")$result
print(head(result))
#>   seqnames   start     end         gene_id score strand
#> 1     chr1 2580559 2583560 ENSG00000228037     .      +
#> 2     chr1 2579559 2582560 ENSG00000284616     .      -
#> 3     chr1 2580559 2583560 ENSG00000260972     .      +
#> 4     chr1 2579559 2582560 ENSG00000226374     .      -
#> 5     chr1 2580559 2583560 ENSG00000232596     .      +