sparse to dense

This function takes h5 or mtx file from cellranger output and convert it in a csv table.

h5tocsv(
  group = c("sudo", "docker"),
  file,
  type = c("h5", "10xgenomics"),
  version = "5"
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

file,

path of the sparse matrix file. For h5 file the full path MUST be included. For mtx matrix the folder MUST contain tsv and mtx files and the FULL path to mtx matrix MUST be provided

type,

h5 refers to h5 files and 10xgenomics to the folder containing barcodes.tsv, genes.tsv and matrix.mtx

version,

cellranger version: 2, 3 or 5.

Value

a dense matrix, with 0s, in csv and txt format

Author

Raffaele Calogero, raffaele [dot] calogero [at] unito [dot] com, University of Torino

Examples