protdatasim function

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

Returns

A data frame with the simulated and attribute metadata.

Examples

data_sim <- protdatasim()
attr(data_sim,"metadata")

norm.200.m100.sd1.vs.m200.sd1_list <- lapply(1:100, protdatasim)
attr(norm.200.m100.sd1.vs.m200.sd1_list[[1]],"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. tools:::Rd_expr_doi("doi:10.1371/journal.pcbi.1010420") .