Read PURPLE QC file

Reads the purple.qc file.

Usage

purple_qc_read(x)

Arguments

x

Path to the purple.qc file.

Value

The input file as a tibble and a summarised tibble with a description of each metric.

Examples

x <- system.file("extdata/purple/purple.qc", package = "gpgr")
(q <- purple_qc_read(x))
#> $raw
#> # A tibble: 10 × 2
#>    key                           value             
#>    <chr>                         <chr>             
#>  1 QCStatus                      WARN_DELETED_GENES
#>  2 Method                        NORMAL            
#>  3 CopyNumberSegments            1428              
#>  4 UnsupportedCopyNumberSegments 0                 
#>  5 Purity                        0.8600            
#>  6 AmberGender                   MALE              
#>  7 CobaltGender                  MALE              
#>  8 DeletedGenes                  7782              
#>  9 Contamination                 0.0               
#> 10 GermlineAberrations           NONE              
#> 
#> $summary
#> # A tibble: 8 × 4
#>       n variable            value                     details                   
#>   <dbl> <chr>               <glue>                    <glue>                    
#> 1     1 QC_Status           WARN_DELETED_GENES        See 'Description'.        
#> 2    13 Method              NORMAL                    Fit method (NORMAL, HIGHL…
#> 3    14 CopyNumberSegments  1428 (Unsupported: 0)     # of CN segments.         
#> 4     2 Purity              0.8600                                              
#> 5    17 Gender              Amber: MALE; Cobalt: MALE                           
#> 6    14 DeletedGenes        7782                      # of homozygously deleted…
#> 7    15 Contamination       0.0                       Rate of contamination in …
#> 8    16 GermlineAberrations NONE                      Can be one or more of: KL…
#>