Data simulation function

Function to simulate benchmark datasets.

protdatasim(
  iii = 1,
  nobs = 200,
  nobs1 = 10,
  ng1 = 5,
  ng2 = 5,
  mg1 = 100,
  mg2 = 200,
  dispg1 = 1,
  dispg2 = 1
)

Arguments

iii	A parameter useful to loop over for simulated lists of datasets. It has no effect.
nobs	Number of peptides
nobs1	Number of peptides with differential expressions between the two conditions
ng1	Number of biological replicates in condition A
ng2	Number of biological replicates in condition B
mg1	Mean in condition A
mg2	Mean in condition B
dispg1	Dispersion in condition A
dispg2	Dispersion in condition B

Value

A data frame with the simulated and attribute metadata.

References

M. Chion, Ch. Carapito and F. Bertrand (2021). Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics. arxiv:2108.07086. https://arxiv.org/abs/2108.07086.

Examples

data_sim <- protdatasim()
attr(data_sim,"metadata")
#>    Sample.name Condition Bio.Rep
#> 1           X1         A       1
#> 2           X2         A       2
#> 3           X3         A       3
#> 4           X4         A       4
#> 5           X5         A       5
#> 6           X6         B       6
#> 7           X7         B       7
#> 8           X8         B       8
#> 9           X9         B       9
#> 10         X10         B      10

norm.200.m100.sd1.vs.m200.sd1_list <- lapply(1:100, protdatasim)
attr(norm.200.m100.sd1.vs.m200.sd1_list[[1]],"metadata")
#>    Sample.name Condition Bio.Rep
#> 1           X1         A       1
#> 2           X2         A       2
#> 3           X3         A       3
#> 4           X4         A       4
#> 5           X5         A       5
#> 6           X6         B       6
#> 7           X7         B       7
#> 8           X8         B       8
#> 9           X9         B       9
#> 10         X10         B      10