Read VIRUSBreakend Summary File

Reads the virusbreakend.vcf.summary.tsv file.

Usage

virusbreakend_summary_read(x)

Arguments

x

Path to virusbreakend.vcf.summary.tsv file.

Value

List with two elements:

• tab: Tibble containing data.

• descr: Description of tibble columns.

Examples

x <- system.file("extdata/virusbreakend/virusbreakend.vcf.summary.tsv", package = "gpgr")
(vb <- virusbreakend_summary_read(x))
#> $tab
#> # A tibble: 1 × 7
#>   Virus                   Length Reads Coverage `Mean depth` Intergrations QC   
#>   <chr>                    <int> <int>    <dbl>        <dbl>         <int> <chr>
#> 1 Human papillomavirus t…   7906  3917     70.4         69.4             4 NA   
#> 
#> $descr
#> # A tibble: 7 × 2
#>   Column       Description                                                
#>   <chr>        <chr>                                                      
#> 1 Virus        Assigned NCBI taxonomy name of viral reference             
#> 2 Length       Length of viral contig                                     
#> 3 Reads        Number of reads mapped to adjusted viral reference         
#> 4 Coverage     Percentage of viral positions with at least one read mapped
#> 5 Mean depth   Mean alignment depth                                       
#> 6 Integrations Number of detected integration breakpoints                 
#> 7 QC           QC status of viral intergrations                           
#>