csvToSparse: csv to Sparse

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

csv to Sparse

Description

This function executes a ubuntu docker that create a sparse matrix, without 0s, from a dense one, including 0s

Usage

csvToSparse(group = c("sudo", "docker"), scratch.folder, file, separator)

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', ','

Value

three files: matrix.mtx, barcodes.tsv and genes.tsv

Author(s)

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

Examples

## Not run: 
system("wget http://130.192.119.59/public/annotated_setPace_10000_noC5.txt.zip")
unzip("annotated_setPace_10000_noC5.txt.zip")
csvToSparse(group="docker", scratch="/data/scratch", 
            file=paste(getwd(), "annotated_setPace_10000_noC5.txt", sep="/"), 
            separator="\t")

## End(Not run)

kendomaniac/CASC documentation built on June 30, 2024, 3:27 a.m.