simulate_data: simulate_data
In jrod55/pseudoDrift: pseudoDrift

View source: R/simulate_data.R

simulate_data

R Documentation

simulate_data

Description

Simulate LC-MS/MS data or any other spectra from sdf db files.

Usage

simulate_data(
  db_ids = NULL,
  compound_names = NULL,
  xls_file_name = NULL,
  valid_sdf_file = NULL,
  nbatch = 3,
  nsamps_per_batch = c(100, 200, 300),
  QC_freq = c(25, 25, 25),
  multiplyer = 100,
  seed = 123,
  sim_sd = NULL,
  m_eff = 1.25,
  b_eff_pos = 1.25,
  b_eff_neg = 0.75,
  save_rds = FALSE,
  rds_name = NULL
)

Arguments

`db_ids`	`character()` ID(s) of compounds to be read from a validated sdf file.
`compound_names`	`character()` Name of the compound(s) to be queried. Not case sensitive, but will only search compounds which begin with the string entered.
`xls_file_name`	`character(1)` Index file in .xls format. This file can be produced using sdf2Index.
`valid_sdf_file`	`character(1)` sdf file to be read. This file can also be produced using sdf2Index.
`nbatch`	`numeric()` Number of batches to simulate.
`nsamps_per_batch`	`numeric()` A numeric vector the same length as 1:nbatch. Number of samples included in each batch to be simulated.
`QC_freq`	`numeric()` A numeric vector the same length as 1:nbatch. Frequency of QC samples.
`multiplyer`	`numeric(1)` value to multiply exact m/z value from MoNA database to have an area measure (default is 1e2)
`seed`	`numeric()` the seed to be used for reproducibility..
`sim_sd`	`numeric()` Standard deviation of simulated data. Default value is 0.25*m/z value after multiplier.
`m_eff`	`numeric()` monotonic effect (slope). Should be >=1.
`b_eff_pos`	`numeric()` batch effect in the positive direction (between batch mean differences). Should be <=1.
`b_eff_neg`	`numeric()` batch effect in the negative direction (between batch mean differences). Should be >=1
`save_rds`	`logical(1)` To write to an rds file.
`rds_name`	`character(1)` Name of the .rds file if save_rds is set to TRUE (default is FALSE).

Value

A nested tibble. The first column is the db id of the compounds simulated. The second column is the simulated matrix. The following four columns represent four batch simulation scenarios, which are:

1) t1_sim_mat - a monotonic (up/down effect) by batch.
2) t2_sim_mat - a batch to batch block effect.
3) t3_sim_mat - random, no systematic change.
4) t4_sim_mat - monotonic and batch to batch block effect.

Examples

sim1 = simulate_data(compound_names = "tricin",
                     xls_file_name = system.file("extdata", "Index.xls", package = "pseudoDrift"),
                     valid_sdf_file = system.file("extdata", "valid-test.sdf", package = "pseudoDrift"))

sim2 = simulate_data(db_ids = c("FIO00738", "FIO00739","FIO00740"),
                     xls_file_name = system.file("extdata", "Index.xls", package = "pseudoDrift"),
                     valid_sdf_file = system.file("extdata", "valid-test.sdf", package = "pseudoDrift"))

## Providing name or compound db IDs gives the same result
identical(sim1,sim2)

jrod55/pseudoDrift documentation built on April 6, 2024, 5:23 a.m.