Combine sparse matrices.

Source: R/dtu_analysis.R

Combine list of sparse count matrices. Presumably coming from import_counts() or import_dge_counts() in conjunction with single-cell data.

combine_to_matrix(
  tx_list,
  cell_extensions = NULL,
  cell_extension_side = "append",
  seurat_obj = NULL,
  tx2gene = NULL,
  assay_name = "dtutx"
)

Arguments

tx_list

List of sparse count matrices, as returned by import_counts() or import_dge_counts() for single-cell data.
cell_extensions

Optional vector of cellname extensions that are added to the cellnames of the samples. The original cellnames and the extension are separated by an underscore '_'. Defaults to an increasing integer per sample.
cell_extension_side

Define to which side of the barcode the cell extensions shall be added ('append' or 'prepend').
seurat_obj

Optional seurat object, where the combined matrix is added as an assay. This has the advantage, that the cells are matched and subsetted if necessary. Currently only Seurat 3 objects are supported.
tx2gene

Optional tx2gene or metadata data frame, can only be used in conjunction with a seurat object. Metadata is added as feature-level meta data to the created assay. The first column of the data frame must contain transcript names/ids. The same transcript names/ids as in the tx_list objects must be used.
assay_name

If the combined matrix should be added to an existing Seurat object, the name of the assay can be specified here.

Value

Either a combined sparse count matrix or a seurat object which the combined sparse count matrix as an assay.

Details

This function adds a cellname extension if necessary. Can optionally add the combined matrix to a existing Seurat object (keeping the cellname extension of the object and matching the cells). Also removes overall non expressed features.

See also

Other DTUrtle DTU: import_counts(), posthoc_and_stager(), priming_bias_detection_probability(), run_drimseq()