load10Xv3: Load 10X Genomics Version 3 Data

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Load 10X Genomics Version 3 Data

Description

Loads 10X Genomics data from a specified directory containing output folders for raw and filtered data. This function is designed to handle data from 10X Genomics Chromium Single Cell technologies (version 3).

Usage

load10Xv3(
  dataDir,
  cellIDs = NULL,
  channelName = NULL,
  readArgs = list(),
  includeFeatures = c("Gene Expression"),
  verbose = TRUE,
  ...
)

Arguments

dataDir	A string specifying the directory that contains the 10X Genomics output folders. This directory should include subdirectories for raw and filtered data, typically named starting with raw_ and filt_, respectively.
cellIDs	An optional vector of cell IDs to include in the loaded data. Default: NULL, indicating that all available cells will be included. This is useful for subsetting the data based on specific cell IDs.
channelName	An optional string specifying the channel name for the data being loaded. This can be used to label the data according to the experimental condition or sample name. Default: NULL.
readArgs	A list of additional arguments to pass to the internal Read10X function used for loading the data. Default: an empty list.
includeFeatures	A character vector specifying which features to include in the loaded data. Common values include "Gene Expression", "Antibody Capture", and "CRISPR Guide Capture". Default: c("Gene Expression").
verbose	A logical flag indicating whether to print progress messages and status updates as the data is loaded. Default: TRUE.
...	Additional arguments passed to other internally called functions, if applicable.

Details

This function provides a comprehensive approach to loading and organizing 10X Genomics data for further analysis. It accommodates the data structure commonly found in 10X Genomics version 3 outputs and allows for the inclusion of various types of molecular data as well as optional cell and channel specifications.

Value

An object of class SoupChannel, representing the loaded 10X data. This object includes raw counts, filtered counts, and optionally, additional metadata and dimensionality reduction coordinates (e.g., t-SNE).

See Also

SoupChannel for the structure and utilities of the SoupChannel class.

Examples

## Not run: 
if (interactive()) {
  # Assuming `dataDir` is the path to your 10X data directory
  channel <- load10Xv3(dataDir = "path/to/10X/data")
  # Now `channel` contains the loaded 10X data as a `SoupChannel` object
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.