mzrtsim: Generate simulated count data with batch effects for npeaks

In yufree/mzrtsim: Raw data (mzML) and peaks list simulation for LC/GC-MS based metabolomics data

Generate simulated count data with batch effects for npeaks

Description

Generate simulated count data with batch effects for npeaks

Usage

mzrtsim(
  ncomp = 100,
  fc = NULL,
  ncond = 2,
  ncpeaks = 0.1,
  nbatch = 3,
  nbpeaks = 0.1,
  npercond = 10,
  nperbatch = c(8, 5, 7),
  batchtype = "mb",
  rtsim = TRUE,
  db = NULL,
  seed = 42
)

Arguments

ncomp	compound numbers to be selected, default 100
fc	fold change of compounds with the same length of compounds numbers, default NULL
ncond	Number of conditions to simulate
ncpeaks	percentage of compounds influenced by conditions
nbatch	Number of batches to simulate
nbpeaks	percentage of peaks influenced by batchs
npercond	Number of samples per condition to simulate
nperbatch	Number of samples per batch to simulate
batchtype	type of batch. 'm' means monotonic, 'b' means block, 'r' means random error, 'mb' means mixed mode of monotonic and block, default 'mb'
rtsim	logical, simulate retention time or not
db	compound database with MS1 data. e.g. hmdbcms or monams1
seed	Random seed for reproducibility

Details

the numbers of batch columns should be the same with the condition columns.

Value

list with rtmz data matrix, row index of peaks influenced by conditions, row index of peaks influenced by batchs, column index of conditions, column of batchs, raw condition matrix, raw batch matrix, peak mean across the samples, peak rsd across the samples

See Also

simdata

Examples

data(hmdbcms)
sim <- mzrtsim(db=hmdbcms)

yufree/mzrtsim documentation built on March 16, 2024, 12:22 p.m.