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

In kendomaniac/CASC: 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

deDetection(
  group = c("sudo", "docker"),
  data.folder,
  counts.table,
  file.type = c("txt", "csv"),
  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
data.folder,	a character string indicating the folder where input data are located and where output will be written
counts.table,	a character string indicating the counts table file. IMPORTANT in the header of the file the covariate group MUST be associated to the column name using underscore, e.g. cell1_cov1
file.type,	type of file: txt tab separated columns csv comma separated columns
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
    system("wget http://130.192.119.59/public/buettner_counts_noSymb.txt.zip")
    unzip("buettner_counts_noSymb.txt.zip")
    lorenzFilter(group="docker", scratch.folder="/data/scratch/",
                data.folder=getwd(), matrixName="buettner_counts_noSymb",
                p_value=0.05, format="txt", separator='\t')

    system("wget ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz")
    system("gzip -d Mus_musculus.GRCm38.92.gtf.gz")
    scannobyGtf(group="docker", data.folder=getwd(),
                 counts.table="lorenz_buettner_counts_noSymb.txt",
                 gtf.name="Mus_musculus.GRCm38.92.gtf",
                 biotype="protein_coding", mt=FALSE, ribo.proteins=FALSE,
                 file.type="txt", umiXgene=3)

    deDetection(group="docker", data.folder=getwd(),
               counts.table="annotated_lorenz_buettner_counts_noSymb.txt",
               file.type="txt", logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4, plot=TRUE)

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.