anovaLike: A function allowing the identification of differentially...

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

A function allowing the identification of differentially expressed genes if multiple groups are provided.

Description

This function executes in a docker edgeR for the identification of differentially expressed genes in bulk RNAseq. IMPORTANT the filename shoould not have any '.' in the name unless .txt

Usage

anovaLike(
  group = c("sudo", "docker"),
  file,
  logFC.threshold = 1,
  FDR.threshold,
  logCPM.threshold = 4,
  plot = c(TRUE, FALSE)
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
file	a character string indicating the path of the file, with counts.table name and extension included
logFC.threshold	minimal logFC present in at least one of the comparisons with respect to reference covariate
FDR.threshold	minimal FDR present in at least one of the comparisons with respect to reference covariate
logCPM.threshold	minimal average abundance
plot	TRUE if differentially expressed genes are represented in a plot.

Author(s)

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino, Italy

Examples

## Not run: 
    #running deDetection
    anovaLike(group="docker", file=paste(getwd(),"annotated_lorenz_buettner_counts_noSymb.txt", sep="/"),
       logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4)

## End(Not run)

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