Export10X: Reexport the data from a Seurat object in 10X format

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Reexport the data from a Seurat object in 10X format

Description

Exports the counts matrix, features and barcodes from a Seurat object in a 10X-like format, with an additional metadata matrix in tsv format, that can be augmented with dimensionality reduction coordinates. The exported data is in standard mtx and tsv formats (sparse matrix matrix market format and tab separated values respectively), which facilitates sharing and reuse, and can be re-imported in a Seurat object with Import10X, or directly in matrices/data frames with e.g. Matrix::readMM and readr::read_tsv.

Usage

Export10X(
  object,
  dir,
  meta_columns = "all",
  append_reductions = "all",
  gzip = T,
  rows = "features.tsv",
  cols = "barcodes.tsv",
  counts = "matrix.mtx",
  meta = "metadata.tsv",
  layer = "counts",
  assay = "RNA"
)

Arguments

object	Seurat object.
dir	character(1). The directory in which the data should be exported. Created if non-existent.
meta_columns	character(n). Metadata columns that should be exported from the Seurat Object. Can also be "all", or empty vector c() for none. Default: "all".
append_reductions	character(n). Name of the dimensionality reductions that should be included with the metadata. Default: "all".
gzip	logical(1). Should the exported files be compressed. If compressed, the filenames are appended with the extension ".gz". Default: TRUE
rows	character(1). Name of the exported file that lists row names. Default: features.tsv
cols	character(1). Name of the exported file that lists column names. Default: barcodes.tsv
counts	character(1). Name of the exported file that contains the sparse raw count matrix. Default: matrix.mtx
meta	character(1). Name of the exported file that contains the metadata. Default: metadata.tsv
layer	character(1). Name of the layer in the Seurat object from which the count matrix is exported. Default: counts
assay	character(1). Name of the assay in the Seurat object from which the count matrix is exported. Default: RNA

Examples

# By default keeping all the metadata columns, and all dimensionality reductions.
Export10X(SeuratObject, "MyDir")
# Include only two custom metadata columns, two dimensionality reductions, and do not compress the matrices.
Export10X(SeuratObject, "MyDir", c("nFeature_RNA", "mito.content"), c("pca","umap"), gzip=FALSE)
# Export normalized CiteSeq data rather than raw RNA counts, and no metadata:
Export10X(SeuratObject, "MyDir", meta_columns = c(), layer="data", assay="CiteSeq")

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.