read.sc.query: Read to memory a query expression matrix

In carmonalab/ProjecTILs: Reference-based analysis of scRNA-seq data

Read to memory a query expression matrix

Description

Load a query expression matrix to be projected onto the reference atlas. Several formats (10x, hdf5, raw and log counts) are supported - see type parameter for details

Usage

read.sc.query(
  filename,
  type = c("10x", "hdf5", "raw", "raw.log2"),
  project.name = "Query",
  min.cells = 3,
  min.features = 50,
  gene.column.10x = 2,
  raw.rownames = 1,
  raw.sep = c("auto", " ", "\t", ","),
  raw.header = TRUE,
  use.readmtx = TRUE
)

Arguments

filename	Path to expression matrix file or folder
type	Expression matrix format (10x, hdf5, raw, raw.log2)
project.name	Title for the project
min.cells	Only keep genes represented in at least min.cells number of cells
min.features	Only keep cells expressing at least min.features genes
gene.column.10x	For 10x format - which column of genes.tsv or features.tsv to use for gene names
raw.rownames	For raw matrix format - A vector of row names, or a single number giving the column of the table which contains the row names
raw.sep	For raw matrix format - Separator for raw expression matrix
raw.header	For raw matrix format - Use headers in expression matrix
use.readmtx	Use ReadMtx function to read in 10x files with custom names

Value

A Seurat object populated with raw counts and normalized counts for single-cell expression

Examples

fname <- "./sample_data"
querydata <- read.sc.query(fname, type="10x")

carmonalab/ProjecTILs documentation built on April 13, 2025, 10:04 p.m.