MitoRiboUmi — mitoRiboUmi • rCASC

This function executes a ubuntu docker showing ribosomal mitochondrial protein genes fraction in each cell

mitoRiboUmi(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  gtf.name,
  bio.type,
  umiXgene
)

Arguments

group,	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder,	a character string indicating the path of the scratch folder
file,	a character string indicating the path of the file, with file name and extension included
separator,	separator used in count file, e.g. '\t', ','
gtf.name,	name for the gtf file tu be used.
bio.type,	ENSEMBL biotype of interest, default for single-cell protein_coding
umiXgene,	a integer defining how many UMI are required to call a gene as present. default: 3

Value

a pdf file called Ribo_mito.pdf

Author

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

if (FALSE) {
   system("wget ftp://ftp.ensembl.org/pub/release-94/gtf/mus_musculus/Mus_musculus.GRCm38.94.gtf.gz")
   system("gzip -d Mus_musculus.GRCm38.94.gtf.gz")
   system("wget http://130.192.119.59/public/testSCumi_mm10.csv.zip")
   unzip("testSCumi_mm10.csv.zip")
   mitoRiboUmi(group="docker", file=paste(getwd(), "testSCumi_mm10.csv", sep="/"), 
                scratch.folder="/data/scratch", separator=",", umiXgene=3, 
                gtf.name="Mus_musculus.GRCm38.94.gtf", bio.type="protein_coding")
}