create_mappability_profile {iimi}

create_mappability_profile

Description

Creates a data frame of start and end positions of the regions that are considered unmappable. Unmappable areas indicate that they can be mapped to another virus segment or a host genome. Note that we only have Arabidopsis Thaliana as a host.

Usage

create_mappability_profile(path_to_bam_files, category, window = 75)

Arguments

path_to_bam_files

Path to the folder that stores the indexed and sorted BAM file(s).

category

Type of unreliable region you are creating. You can use categories in the provided unreliable_regions data frame or customize in your own way.

window

The sliding window size of your choice. Default is 75.

Value

A data frame of start and end positions of the regions that are considered unmappable.

Examples

## Not run: 
## Please change the path to your folder where you store the mapped viruses
mappability_profile <- create_mappability_profile("path/to/folder",
  category = "Unmappable regions")

## End(Not run)