FDL: fetch, decompress and load the quantification result of a...

In COMBINE-lab/roe: R utilities for alevin-fry

fetch, decompress and load the quantification result of a specific dataset as a SingleCellExperiment object and store it in the sce slot of the returned processed_quant list.

Description

fetch, decompress and load the quantification result of a specific dataset as a SingleCellExperiment object and store it in the sce slot of the returned processed_quant list.

Usage

FDL(
  dataset_id,
  tar_dir = "quant_tar",
  tar_name = NULL,
  quant_dir = "processed_quant",
  quant_path_name = NULL,
  output_format = "scRNA",
  nonzero = FALSE,
  force = FALSE,
  quiet = FALSE
)

Arguments

dataset_id	the id of an available dataset. Run print_available_datasets() for all available datasets.
tar_dir	a string to a path where the fetched tar files will be stored. It will be created if does not exist.
tar_name	a string indicates the name of the tar file. If NULL, the dataset_id will be used as the file name.
quant_dir	a string to a path where the fetched tar files will be stored. It will be created if does not exist.
quant_path_name	a string indicates the name of the directory that will be used for storing the quantification result. If NULL, the dataset_id will be used as the file name.
output_format	the format of the returned SingleCellExperiement object. It will be passed to loadFry as the outputFormat parameter.
nonzero	It will be passed to loadFry as the nonzero parameter.
force	logic whether to proceed if the files exist.
quiet	logical whether to display no messages

Value

A complete ProcessedQuant class object with valid tar_path, quant_path and sce slots.

COMBINE-lab/roe documentation built on Nov. 8, 2022, 5:23 p.m.