experimentPower: A wrapper function for experiment_power from RnaSeqSampleSize...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A wrapper function for experiment_power from RnaSeqSampleSize Bioconductor package

Description

This function evaluate the statistical power of a pilot experiment

Usage

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(s)

Raffaele Calogero

Examples

## Not run: 
 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)

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.