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

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

A function allowing the identification of differentially expressed genes.

Description

This function executes in a docker edgeR for the idnetification of differentially expressed genes in single-cells RNAseq

Usage

anovaLike(
  group = c("sudo", "docker"),
  file,
  sep,
  cluster.file,
  ref.cluster,
  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 counts table file with the path of the file.
sep	separator used in count file, e.g. '\t', ','
cluster.file	a character string indicating the _clustering.output.txt file of interest, generated by bootstrapSimlar or bootStrapTsne. IMPORTANT this file miust be located in the same folder where counts.table is placed
ref.cluster	a number indicating the cluster to be used a reference for anova-like comparison with the other clusters.
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	boolean, TRUE a plot of differentially expressed genes is generated

Value

Three tab delimited files file with prefix DE\_, filtered\_DE\_, logFC\_filtered\_DE\_ followed by the counts table name, the count table, reordered on the basis of cluster positions, has the extension \_reordered.txt

Author(s)

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

Examples

## Not run: 
    #running deDetection
system("wget http://130.192.119.59/public/annotated_setPace_10000_noC5_clustering.output.txt")
system("wget http://130.192.119.59/public/annotated_setPace_10000_noC5.txt.zip")
unzip("annotated_setPace_10000_noC5.txt.zip")
anovaLike(group="docker", file=paste(getwd(),"annotated_setPace_10000_noC5.txt",sep="/"),
       sep="\t", cluster.file="annotated_setPace_10000_noC5_clustering.output.txt", ref.cluster=3,
       logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4, plot=TRUE)


## End(Not run)

kendomaniac/rCASC documentation built on June 10, 2025, 2:52 a.m.