A wrapper function for experiment_power from RnaSeqSampleSize Bioconductor package

This function evaluate the statistical power of a pilot experiment

experimentPower(
  group = c("sudo", "docker"),
  filename,
  replicatesXgroup = 3,
  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

replicatesXgroup,

an integer indicating the number of samples used in each group

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: 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)
 experimentPower(group="docker",filename="_counts.txt",replicatesXgroup=7,
 FDR=0.1, genes4dispersion=200, log2fold.change=1)
}