Calculate Delta Variance (Pseudoreplication Bias Metric) — calc_delta

Measures the difference in gene expression variance between true biological replicates and cell-shuffled pseudoreplicates (Squair et al., Nature Communications 2021). Positive delta variance indicates that biological replicates have higher inter-individual variability than randomly pooled pseudoreplicates.

Usage

calc_delta_variance(
  counts,
  replicates,
  conditions,
  cell_types = NULL,
  n_perm = 3
)

Arguments

counts: Count matrix (features x cells).
replicates: Factor of biological replicate / batch assignments for each cell.
conditions: Factor of condition or cell-type labels.
cell_types: Optional cell type vector to evaluate per cell type or overall.
n_perm: Number of permutation shuffles to compute mean pseudoreplicate variance. Default is 3.

Value

A named list:

delta_variance: Numeric vector of gene-level delta variance values
mean_delta_variance: Mean delta variance across all genes
median_delta_variance: Median delta variance across all genes

Examples

data(example_scrna, package = "scSimEval")
calc_delta_variance(example_scrna$ref,
                    replicates = example_scrna$batch_info,
                    conditions = example_scrna$cell_types)
#> $delta_variance
#>     Gene_01     Gene_02     Gene_03     Gene_04     Gene_05     Gene_06 
#> -16155008.8  -1636401.7  -3217284.6   1043935.4  28050446.3  -5968890.8 
#>     Gene_07     Gene_08     Gene_09     Gene_10     Gene_11     Gene_12 
#>   3998925.2   7160951.9  33175563.1 -43255329.8  10112846.1 -51418749.5 
#>     Gene_13     Gene_14     Gene_15     Gene_16     Gene_17     Gene_18 
#>   3400725.0  -7527716.7  -2618645.0 -10938126.4  15667286.3  -1510473.8 
#>     Gene_19     Gene_20     Gene_21     Gene_22     Gene_23     Gene_24 
#>   5355085.9 -31251620.3   7531808.3   2241971.0   7880542.7   9885499.6 
#>     Gene_25     Gene_26     Gene_27     Gene_28     Gene_29     Gene_30 
#>   4264460.2  -1244888.5 -18829827.2   2064205.6   2216219.6  -1199391.8 
#>     Gene_31     Gene_32     Gene_33     Gene_34     Gene_35     Gene_36 
#>  -3482214.5   3366685.3   9441161.7  -4744896.3   9392338.4   3216843.2 
#>     Gene_37     Gene_38     Gene_39     Gene_40     Gene_41     Gene_42 
#>   5197981.1   9263225.1    881787.3   1314003.0 -21746643.5  -8603791.9 
#>     Gene_43     Gene_44     Gene_45     Gene_46     Gene_47     Gene_48 
#>    722862.9   6673800.6   3324635.1 -31188112.0   1616807.6  -2808888.7 
#>     Gene_49     Gene_50     Gene_51     Gene_52     Gene_53     Gene_54 
#> -26304833.4  24362120.1   7920296.3 -29113246.0  16549957.5   7563376.2 
#>     Gene_55     Gene_56     Gene_57     Gene_58     Gene_59     Gene_60 
#>   5970251.3 -21632226.4 -25848713.7  -6401459.6    330397.8   3707688.8 
#> 
#> $mean_delta_variance
#> [1] -1896345
#> 
#> $median_delta_variance
#> [1] 1465405
#>