import_dataset_and_model: Converts a single-cell dataset to an scDissector LDM object
In effiken/scDissector: Exploratory Data Analysis tool for single-cell RNA-seq data

View source: R/load_dataset_and_model.R

import_dataset_and_model

R Documentation

Converts a single-cell dataset to an scDissector LDM object

Description

Converts a single-cell dataset to an scDissector LDM object

Usage

import_dataset_and_model(model_version_name, clustering_data_path, umitab,
  cell_to_cluster, cell_to_sample, min_umis = 250, max_umis = 25000,
  ds_numis = c(200, 500, 1000, 2000), insilico_gating = NULL,
  clustAnnots = NA, ds_list = NULL)

Arguments

`model_version_name`	user-defined model version name
`clustering_data_path`	scDissector clustering_data folder. An empty folder could be created by create_clustering_data_dir
`umitab`	UMI matrix. Genes are rows while cells are columns. row names are the gene IDs (usually geneSymbols) and column names are cell IDs.
`cell_to_cluster`	a vector that maps from cells IDs to cluster IDs. The vector names are the cell IDs while clusters IDs are the vector values.
`cell_to_sample`	a vector that maps from cells IDs to sample IDs. The vector names are the cell IDs while sample IDs are the vector values.
`min_umis`	lower UMI-count threshold
`max_umis`	upper UMI-count threshold
`ds_numis`	[optional] vector containing UMI counts to down-sample the dataset to.
`insilico_gating`	[optional] A list containing the in-silico gating policy for the imported cells. Each item in the list is a list containg two parameters: (1) genes- a vector defining a gene list (2) interval - a vector of length 2 defining the lower and upper UMI fraction expressed by the input gene list.
`ds_list`	[optional] user-defined downsapling
`excluded_clusters`	[optional] vector with clusters to exclude. Cells associated with these clusters are not loaded.
`clustAnnots=NA`	[optional] cluster annotations vector. Mapping from cluster IDs to user-defined annotations.