ExportGenotype: Reexport vartrix matrices from a genotype object

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

Reexport vartrix matrices from a genotype object

Description

Exports the reference and alternate count matrices, as well as the barcodes (colnames), variant names (rownames) and metadata/reference genotypes.

Usage

ExportGenotype(
  genotype,
  dir,
  meta_columns = "all",
  append_genotypes = T,
  gzip = T,
  rows = "vartrix_variants.tsv",
  cols = "vartrix_barcodes.tsv",
  ref_counts = "vartrix_ref_matrix.mtx",
  alt_counts = "vartrix_alt_matrix.mtx",
  meta = "vartrix_metadata.tsv"
)

Arguments

genotype	A genotype 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 genotype Object. Can also be "all", or empty vector c() for none. Default: "all".
append_genotypes	logical(1). Whether the bulk genotypes should also be exported (appended to metadata). Default: TRUE.
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: vartrix_variants.tsv
cols	character(1). Name of the exported file that lists column names. Default: vartrix_barcodes.tsv
ref_counts	character(1). Name of the exported file that contains the reference allele sparse raw count matrix. Default: vartrix_ref_matrix.mtx
alt_counts	character(1). Name of the exported file that contains the alternate allele sparse raw count matrix. Default: vartrix_alt_matrix.mtx
meta	character(1). Name of the exported file that contains the metadata. Default: metadata.tsv

Examples

# By default keeping all the metadata columns, and no 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)

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