modalities_load_cellranger_count: Load Cell Ranger data and divide by modality

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

Load Cell Ranger data and divide by modality

Description

Load Cell Ranger data and divide by modality

Usage

modalities_load_cellranger_count(
  path,
  modalities = c("RNA", "ADT", "HTO"),
  folder = "outs/raw_feature_bc_matrix",
  hto.pattern = "^hto",
  gex.listname = "Gene Expression",
  adt.listname = "Antibody Capture"
)

Arguments

path	Path to cellranger output (outs) folder
modalities	Vector of modalities to be extracted from Cell Ranger output
folder	Folder containing count matrix (raw_feature_bc_matrix or filtered_feature_bc_matrix)
hto.pattern	Pattern in feature name distinguishing hastag (HTOs) from other antibody derived tags (ADTs)
gex.listname	Name of dataframe containing gene expression counts (after Seurat::Read10X)
adt.listname	Name of dataframe containing ADT counts (after Seurat::Read10X)

Value

list of modality count matrices

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.