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

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

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

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

Examples

if (FALSE) {
    #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)
}