meta_info: Define Meta Information of A Dataset
In duohongrui/simutils: Common functions used in data simulation and evaluation

meta_info

R Documentation

Define Meta Information of A Dataset

Description

Define Meta Information of A Dataset

Usage

meta_info(
  id,
  repository = NULL,
  accession_number = NULL,
  URL = NULL,
  platform,
  species,
  organ = NULL,
  cell_num,
  gene_num,
  data_type = "count",
  ERCC = FALSE,
  dilution_factor = NULL,
  volume = NULL,
  group_condition = NULL,
  treatment = NULL,
  batch_info = NULL,
  cluster_info = NULL,
  spatial_coordinate = NULL,
  start_cell = NULL
)

Arguments

`id`	Dataset ID
`repository`	Which repository or cloud contains the dataset, e.g. GEO, ArrayExpress.
`accession_number`	The accession number in the repository if available.
`URL`	The URL to downloiad the dataset.
`platform`	Sequencing platform.
`species`	Organism.
`organ`	Which source or organ do the samples come from?
`cell_num`	The cell number of the dataset.
`gene_num`	The gene number of the dataset.
`data_type`	Which type is the dataset? e.g. count, FPKM.
`ERCC`	Whether the dataset contains ERCC spike-in genes?
`dilution_factor`	If there are spike-in genes, dilution factor is neccessary.
`volume`	The volume (nanoliter) of mix liquid used in experiment.
`group_condition`	Vector. The group assignment of cells in the dataset.
`treatment`	Vector. The treatment of cells in the experiment.
`batch_info`	Vector. The batch information of cells in the experiment.
`cluster_info`	Vector. The cluster information of cells.
`spatial_coordinate`	A data frame of x and y coordinates of spatial transcriptomics data
`start_cell`	The cell id which is determined as the start_cell of a trajectory