sampleSize: A wrapper function for sample_size_distribution function from...

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

A wrapper function for sample_size_distribution function from RnaSeqSampleSize Bioconductor package

Description

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

Usage

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(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)
   sampleSize(group="docker", filename="_counts.txt", power=0.80, FDR=0.1,
   genes4dispersion=200, log2fold.change=1)

## End(Not run)

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