mitoRiboUmi.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
a pdf file called Ribo_mito.pdf
Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
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") }