A wrapper function for deseq2 for two groups only

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.

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

Raffaele Calogero

Examples

if (FALSE) {
    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)

}