designSampleSizePTM: Planning future experimental designs of PTM experiments in...

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Planning future experimental designs of PTM experiments in sample size calculation

Description

Calculate sample size for future experiments of a PTM experiment based on intensity-based linear model. Calculation is only available for group comparison experimental designs (not including time series). Two options of the calculation: (1) number of biological replicates per condition, (2) power.

Usage

designSampleSizePTM(
  data,
  desiredFC,
  FDR = 0.05,
  numSample = TRUE,
  power = 0.8,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  base = "MSstatsPTM_log_"
)

Arguments

data	output of the groupComparisonPTM function.
desiredFC	the range of a desired fold change which includes the lower and upper values of the desired fold change.
FDR	a pre-specified false discovery ratio (FDR) to control the overall false positive rate. Default is 0.05
numSample	minimal number of biological replicates per condition. TRUE represents you require to calculate the sample size for this category, else you should input the exact number of biological replicates.
power	a pre-specified statistical power which defined as the probability of detecting a true fold change. TRUE represent you require to calculate the power for this category, else you should input the average of power you expect. Default is 0.9
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing will be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If append = TRUE, has to be a valid path to a file.
base	start of the file name.

Details

The function fits the model and uses variance components to calculate sample size. The underlying model fitting with intensity-based linear model with technical MS run replication. Estimated sample size is rounded to 0 decimal. The function can only obtain either one of the categories of the sample size calculation (numSample, numPep, numTran, power) at the same time.

Value

data.frame - sample size calculation results including varibles: desiredFC, numSample, FDR, and power.

Examples

model.lf.msstatsptm = groupComparisonPTM(summary.data, 
                                     data.type = "LabelFree",
                                     verbose = FALSE)
                                     
#(1) Minimal number of biological replicates per condition
designSampleSizePTM(data=model.lf.msstatsptm, numSample=TRUE,
                 desiredFC=c(2.0,2.75), FDR=0.05, power=0.8)
#(2) Power calculation
designSampleSizePTM(data=model.lf.msstatsptm, numSample=5,
                 desiredFC=c(2.0,2.75), FDR=0.05, power=TRUE)                                  

Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.