scRead: scRead function

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

scRead function

Description

A function to read single-cell expression matrix

Usage

scRead(
  sample_name = NULL,
  data_dir = NULL,
  gene_column = 2,
  min_cells = 5,
  min_features = 200,
  min_rnas = 1000,
  percent_mito = 20,
  mito_pattern = "^GRCh38_MT-|^mm10___mt-|^MT-|^mt-",
  project_name = "Seurat",
  group_name = NULL,
  strip_suffix = TRUE,
  meta_file = NULL,
  human.prefix = "GRCh38_",
  mouse.prefix = "mm10___",
  organism.thres = 0.9,
  organism.use = NULL,
  meta_features = NULL
)

Arguments

sample_name	Name of the sample
data_dir	Directory containing the quantification matrix (matrix.mtx, features.tsv, and barcodes.tsv)
gene_column	Column of genes.tsv to use for gene names, default is 2
min_cells	Minimum number of cells express this feature
min_features	Minimum number of features expressed in this cell
min_rnas	Minimum number of molecules detected within a cell.
percent_mito	Maximum percent of mito in a cell
mito_pattern	regex pattern for mitochondrial genes, default is '^GRCh38_MT-|^mm10___mt-|^MT-|^mt-'
project_name	Project name for the Seurat object
group_name	Group name for the Seurat object
strip_suffix	Remove trailing '-1' in cell barcodes
meta_file	Meta file to use
human.prefix	The prefix denoting rownames for human cells. Default is 'GRCh38_'. Just for PDX samples
mouse.prefix	The prefix denoting rownames for mouse cells. Default is 'mm10___'. Just for PDX samples
organism.thres	Threshould fraction of reads to separate organism and background, Default is 0.9. Just for PDX samples
organism.use	Which organism is used. Default is NULL, means all organisms will be used. Just for PDX samples
meta_features	Features used to store in the meta.data slot

Details

read scRNA matrix

It supports read gene expression matrix and microbiome quantification matrix simultaneously

Value

A Seurat object.

References

Inspired by Stuart and Butler et al, Cell (2019)

Examples

x <- scRead(sample_name = "Infected", 
  data_dir = system.file("extdata/H3N2_10X_matrix/Infected/",
                         package="Yeskit"), 
  gene_column = 2, 
  project_name = "H3N2", 
  group_name = "Infected",
  meta_file = system.file("extdata/H3N2_10X_matrix/Infected/microbes.tsv",
                          package="Yeskit"),
)    
x

ncrna/Yeskit documentation built on Nov. 4, 2024, 10:32 p.m.