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Compute the Gini index of each sample

Source: R/quality_control.R
compute_gini.Rd

Computes the Gini index of the barcode counts of each sample, a measure of how evenly the reads are distributed over the barcodes of the library. It is 0 when all the barcodes have the same number of reads and close to 1 when a few barcodes take most of the reads. A Gini index that increases strongly over time or differs between replicates can indicate a bottleneck or a technical problem. Use plot_gini to plot it.

Usage

compute_gini(screenR_Object)

Arguments

screenR_Object

The ScreenR object obtained using create_screenr_object.

Value

A tibble with the columns Sample and Gini.

See also

plot_gini, barcode_lost

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
compute_gini(object)
#> # A tibble: 14 × 2
#>    Sample       Gini
#>    <fct>       <dbl>
#>  1 T1          0.420
#>  2 T2          0.434
#>  3 Time3_TRT_A 0.445
#>  4 Time3_TRT_B 0.445
#>  5 Time3_TRT_C 0.443
#>  6 Time3_A     0.438
#>  7 Time3_B     0.441
#>  8 Time3_C     0.444
#>  9 Time4_TRT_A 0.477
#> 10 Time4_TRT_B 0.482
#> 11 Time4_TRT_C 0.483
#> 12 Time4_A     0.470
#> 13 Time4_B     0.467
#> 14 Time4_c     0.471