scRead: scRead function

Description Usage Arguments Details Value Author(s)

View source: R/scRead.R

Description

A function to read single-cell expression matrix

Usage

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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.

Author(s)

Wei Zhang


rstatistics/SCKIT documentation built on Dec. 22, 2021, 7:18 p.m.