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ReadMtx

Load in data from remote or local mtx files

Description

Enables easy loading of sparse data matrices

Usage

ReadMtx(
  mtx,
  cells,
  features,
  cell.column = 1,
  feature.column = 2,
  skip.cell = 0,
  skip.feature = 0,
  unique.features = TRUE,
  strip.suffix = FALSE
)

Arguments

mtx

Name or remote URL of the mtx file
cells

Name or remote URL of the cells/barcodes file
features

Name or remote URL of the features/genes file
cell.column

Specify which column of cells file to use for cell names; default is 1
feature.column

Specify which column of features files to use for feature/gene names; default is 2
skip.cell

Number of lines to skip in the cells file before beginning to read cell names
skip.feature

Number of lines to skip in the features file before beginning to gene names
unique.features

Make feature names unique (default TRUE)
strip.suffix

Remove trailing "-1" if present in all cell barcodes.

Value

A sparse matrix containing the expression data.

Examples

## Not run: 
# For local files:

expression_matrix <- ReadMtx(
  mtx = "count_matrix.mtx.gz", features = "features.tsv.gz",
  cells = "barcodes.tsv.gz"
)
seurat_object <- CreateSeuratObject(counts = expression_matrix)

# For remote files:

expression_matrix <- ReadMtx(mtx = "http://localhost/matrix.mtx",
cells = "http://localhost/barcodes.tsv",
features = "http://localhost/genes.tsv")
seurat_object <- CreateSeuratObject(counts = data)

## End(Not run)
Seurat

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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