A wrapper function for sample_size_distribution function from RnaSeqSampleSize Bioconductor package

This function executes sample_size_distribution to identify the number of samples x group needed to obtain a specific statistical power

sampleSize(
  group = c("sudo", "docker"),
  filename,
  power = 0.8,
  FDR = 0.1,
  genes4dispersion = 200,
  log2fold.change = 1,
  output.folder = getwd()
)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

filename,

a character string indicating the name of the count table file

power,

expected statistical power required to detect prognostic genes

FDR,

false discovery rate

genes4dispersion,

an integer indicating the number of genes used in estimation of read counts and dispersion distribution

log2fold.change,

an integer indicating the minimum log2 fold change for prognostic genes between two groups

output.folder,

a string indicating the path where to save the output file

Value

a string with the requested informations. the string is also saved in a file: sample_size_evaluation.txt , power_evaluation.txt

Author

Raffaele Calogero

Examples

if (FALSE) {
   system("wget 130.192.119.59/public/test.analysis.zip")
   unzip("test.analysis.zip")
   setwd("test.analysis")
   library(docker4seq)
   sampleSize(group="docker", filename="_counts.txt", power=0.80, FDR=0.1,
   genes4dispersion=200, log2fold.change=1)
}