read_matrix

besca.st.read_matrix(root_path, citeseq=None, annotation=True, use_genes='SYMBOL', species='human')[source]

Read matrix file as expected for the standard workflow.

Parameters:

  • root_path (str) –

    root path of the analysis. Expected in this folder a raw folder containing containg the matrix.mtx, genes.tsv,

    barcodes.tsv and if applicable metadata.tsv

  • annotation (bool (default = True)) – boolian identifier if an annotation file is also located in the folder and should be added to the AnnData object

  • use_genes (str) – either SYMBOL or ENSEMBL. Other genenames are not yet supported.

  • species (str | default = ‘human’) – string specifying the species, only needs to be used when no Gene Symbols are supplied and you only have the ENSEMBLE gene ids to perform a lookup.

  • citeseq ('gex_only' or 'citeseq_only' or False or None | default = None) – string indicating if only gene expression values (gex_only) or only protein expression values (‘citeseq_only’) or everything is read if None is specified

Return type:

returns an AnnData object