deTwoGroups.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deTwoGroups.R
\name{deTwoGroups}
\alias{deTwoGroups}
\title{A function allowing the identification of differentially expressed genes.}
\usage{
deTwoGroups(group = c("sudo", "docker"), file)
}
\arguments{
\item{group, }{a character string. Two options: sudo or docker, depending to which group the user belongs}

\item{file, }{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}
}
\description{
This function executes in a docker edgeR for the idnetification of differentially expressed genes in single-cells RNAseq
}
\examples{
\dontrun{
    #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)
}

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