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read_10x_mtx

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read_10x_mtx#

muon.read_10x_mtx(path: PathLike, extended: bool = True, *args, **kwargs) → MuData#

Read data from 10X Genomics-formatted files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz)

This function uses scanpy.read_10x_mtx() internally and patches its behaviour to: - attempt to read interval field for features; - (for ATAC-seq) attempt to locate peak annotation file and add peak annotation; - (for ATAC-seq) attempt to locate fragments file.

Parameters:

  • path (str) – Path to 10X folder (filtered_feature_bc_matrix or raw_feature_bc_matrix) or to the matrix file inside it

  • extended (bool, optional (default: True)) – Perform extended functionality automatically such as locating peak annotation and fragments files.

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