Gather all count sketches into a single count sketch matrix

Usage

BascetGatherCountSketch(
  bascetRoot,
  inputName = "countsketch",
  outputName = "countsketch_mat.csv",
  includeCells = NULL,
  kmerSize = 31,
  sketchSize = 4096,
  overwrite = FALSE,
  numLocalThreads = NULL,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

inputName

Name of input shard

outputName

Name of output file

includeCells

List of cells to process

kmerSize

KMER length to use

sketchSize

Size of the count sketch. Must be a power of two

overwrite

Force overwriting of existing files. The default is to do nothing files exist

numLocalThreads

Number of threads to use per job. Default is the number from the runner

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance

TODO produce a binary file format instead; gather files upon loading?

Value

A job to be executed, or being executed, depending on runner settings