wrapperDeseq2: A wrapper function for deseq2 for two groups only

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

A wrapper function for deseq2 for two groups only

Description

This function runs deseq2 on a table genrated with sample2experiment having the covariates added in the names of the columns, separated by the names with underscore.

Usage

wrapperDeseq2(
  output.folder,
  group = c("sudo", "docker"),
  experiment.table,
  log2fc = 1,
  fdr = 0.1,
  ref.covar = "0",
  type = c("gene", "isoform", "mirna"),
  batch = FALSE
)

Arguments

output.folder	a character string indicating where the tables generated by samples2experiment are located and were results will be placed
group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
experiment.table	a character string indicating the counts table generated with sample3experiment with addition of covariates
log2fc	log2fc threshold for differetially expressed genes
fdr	fdr threshold
ref.covar	covariate to be used as reference
type	character with three options: gene, isoform, mirna. if gene is used two files are generated for geneset enrichment, the filtered Gene symbols and the background that contains all gene simbols.
batch	logical FALSE, TRUE

Value

Returns a full table of differentially expressed genes (prefix DEfull), a filtered table of differentially expressed genes (prefix DEfiltered) and the normalized counts table (prefix normalized)

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)
    wrapperDeseq2(output.folder=getwd(), group="docker", experiment.table="_counts.txt", log2fc=1,
    fdr=0.1, ref.covar="Cov.1", type="gene", batch=FALSE)


## End(Not run)

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