tenx_load_qc: Load 10X data

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Load 10X data

Description

Load 10X data

Usage

tenx_load_qc(
  path_10x = "",
  h5_file = "",
  frag_file = stringr::str_replace(h5_file, "filtered_feature_bc_matrix.h5",
    "atac_fragments.tsv.gz"),
  min_cells = 5,
  min_features = 800,
  mt_pattern = "^mt-|^MT-",
  species_pattern = "",
  exp_type = "GEX",
  remove_species_pattern = TRUE,
  violin_plot = TRUE,
  sample_name = path_10x
)

Arguments

path_10x	Path to 10X RNAseq data "filtered_feature_bc_matrix" folder
h5_file	Path to 10X h5 file
frag_file	Path to 10X ATAC fragments file. Only required for ATAC data
min_cells	Passed to CreateSeuratObject: Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
min_features	Passed to CreateSeuratObject: Include cells where at least this many features are detected.
mt_pattern	Pattern used to identify mitochondrial reads (eg, "^MT-" Must add species_pattern if remove_species_pattern = FALSE (eg, "^hg19-MT-" or "^hg19-MT-|^mm10-mt-")
species_pattern	Pattern used to select only reads from a single species (eg, "^mm10-" or "^hg19-")
exp_type	Experiment type (one of "GEX", "ATAC" or "GEX+ATAC")
remove_species_pattern	Specifies if want to remove species_pattern prefix from gene names. If TRUE (default), removes species_pattern prefix.
violin_plot	If TRUE (default), produces a violin plot
sample_name	Sample name. Used in violin plots for title

Value

A Seurat

Examples

## Not run: 
seurat_obj <- tenXLoadQC("path/to/10X/data/", species_pattern = "^mm9-")

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.