# How to convert R matrix to anndata

**URL:** <https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427>\
**Category:** Help\
**Tags:** scvi, anndata\
**Created:** [January 15, 2025, 10:55pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427 "2025-01-15T22:55:53Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Slack90](https://avatars.discourse-cdn.com/v4/letter/s/aeb1de/32.png) [@Slack90](https://discourse.scverse.org/u/Slack90)\
**Post date:** [January 15, 2025, 10:55pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427/1 "2025-01-15T22:55:53Z")

</div>

Hi,

I want to processed the raw RNAseq data deposited here in as “GSE165371\_cb\_adult\_mouse.tar.gz” [GEO Accession viewer](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165371)

Here a screenshot of the folder content:

 ![image](https://canada1.discourse-cdn.com/flex035/uploads/forum11/original/2X/0/07e9ca4fdc601d36d5699d8a56ec79de7b5cfb96.png)

As tiy can see it contains two text files and a .matrix file.  
I want to use python for further processing, so I need to convert their raw data from .matrix to anndata object. Does anyone know how to do it? I previously converted a Seurat object into AnnData, but I am not sure what to do when starting from a .matrix

---

<div class="post-metadata">

**Author:** ![gtca](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/gtca/32/1199_2.png) [@gtca](https://discourse.scverse.org/u/gtca)\
**Post date:** [January 15, 2025, 11:37pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427/2 "2025-01-15T23:37:52Z")

</div>

Hey @Slack90,

I think [`scanpy.read_10x_mtx()`](https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_10x_mtx.html) is what you’re looking for — it will load gene / cell IDs as well when all three files are in one folder.

---

<div class="post-metadata">

**Author:** ![Slack90](https://avatars.discourse-cdn.com/v4/letter/s/aeb1de/32.png) [@Slack90](https://discourse.scverse.org/u/Slack90)\
**Post date:** [January 16, 2025, 3:13pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427/3 "2025-01-16T15:13:23Z")

</div>

Thanks for the reply

Yes that seems pretty much what I was looking for, however when I tested it, I got into some issue, I tried to rename the files, so they contain the suffix \_matrix:

```auto
adata = sc.read_10x_mtx('/home/GSE165371_cb_adult_mouse/', prefix = 'cb_adult_mouse_', cache_compression= 'gzip')

```

But I get the error:

```auto

---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[6], line 1
----> 1 adata = sc.read_10x_mtx('/home/slacava3/data_jkebsch1/salvo/Xenopus_levis/code/GSE165371_cb_adult_mouse/', prefix = 'cb_adult_mouse_', cache_compression= 'gzip')

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/legacy_api_wrap/ __init__.py:82, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
     79 @wraps(fn)
     80 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
     81 if len(args_all) <= n_positional:
---> 82 return fn(*args_all, **kw)
     84 args_pos: P.args
     85 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/scanpy/readwrite.py:561, in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only, prefix)
    559 prefix = "" if prefix is None else prefix
    560 is_legacy = (path / f"{prefix}genes.tsv").is_file()
--> 561 adata = _read_10x_mtx(
    562 path,
    563 var_names=var_names,
    564 make_unique=make_unique,
    565 cache=cache,
    566 cache_compression=cache_compression,
    567 prefix=prefix,
    568 is_legacy=is_legacy,
    569 )
    570 if is_legacy or not gex_only:
    571 return adata

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/scanpy/readwrite.py:595, in _read_10x_mtx(path, var_names, make_unique, cache, cache_compression, prefix, is_legacy)
    589 suffix = "" if is_legacy else ".gz"
    590 adata = read(
    591 path / f"{prefix}matrix.mtx{suffix}",
    592 cache=cache,
    593 cache_compression=cache_compression,
    594 ).T # transpose the data
--> 595 genes = pd.read_csv(
    596 path / f"{prefix}{'genes' if is_legacy else 'features'}.tsv{suffix}",
    597 header=None,
    598 sep="\t",
    599 )
    600 if var_names == "gene_symbols":
    601 var_names_idx = pd.Index(genes[1].values)

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1026, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)
   1013 kwds_defaults = _refine_defaults_read(
   1014 dialect,
   1015 delimiter,
   (...)
   1022 dtype_backend=dtype_backend,
   1023 )
   1024 kwds.update(kwds_defaults)
-> 1026 return _read(filepath_or_buffer, kwds)

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py:620, in _read(filepath_or_buffer, kwds)
    617 _validate_names(kwds.get("names", None))
    619 # Create the parser.
--> 620 parser = TextFileReader(filepath_or_buffer, **kwds)
    622 if chunksize or iterator:
    623 return parser

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1620, in TextFileReader. __init__ (self, f, engine, **kwds)
   1617 self.options["has_index_names"] = kwds["has_index_names"]
   1619 self.handles: IOHandles | None = None
-> 1620 self._engine = self._make_engine(f, self.engine)

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1880, in TextFileReader._make_engine(self, f, engine)
   1878 if "b" not in mode:
   1879 mode += "b"
-> 1880 self.handles = get_handle(
   1881 f,
   1882 mode,
   1883 encoding=self.options.get("encoding", None),
   1884 compression=self.options.get("compression", None),
   1885 memory_map=self.options.get("memory_map", False),
   1886 is_text=is_text,
   1887 errors=self.options.get("encoding_errors", "strict"),
   1888 storage_options=self.options.get("storage_options", None),
   1889 )
   1890 assert self.handles is not None
   1891 f = self.handles.handle

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/io/common.py:765, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
    761 if compression == "gzip":
    762 if isinstance(handle, str):
    763 # error: Incompatible types in assignment (expression has type
    764 # "GzipFile", variable has type "Union[str, BaseBuffer]")
--> 765 handle = gzip.GzipFile( # type: ignore[assignment]
    766 filename=handle,
    767 mode=ioargs.mode,
    768 **compression_args,
    769 )
    770 else:
    771 handle = gzip.GzipFile(
    772 # No overload variant of "GzipFile" matches argument types
    773 # "Union[str, BaseBuffer]", "str", "Dict[str, Any]"
   (...)
    776 **compression_args,
    777 )

File ~/.conda/envs/MyEnv/lib/python3.11/gzip.py:174, in GzipFile. __init__ (self, filename, mode, compresslevel, fileobj, mtime)
    172 mode += 'b'
    173 if fileobj is None:
--> 174 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
    175 if filename is None:
    176 filename = getattr(fileobj, 'name', '')

FileNotFoundError: [Errno 2] No such file or directory: '/home/cb_adult_mouse_features.tsv.gz'

```

Fistly I had the issue that it could not find “feature” file, so I changed “cb\_adult\_mouse\_genes” to “cb\_adult\_mouse\_features” . But now I have the issue of no .tsv file found (where it should be .csv)

---

<div class="post-metadata">

**Author:** ![Slack90](https://avatars.discourse-cdn.com/v4/letter/s/aeb1de/32.png) [@Slack90](https://discourse.scverse.org/u/Slack90)\
**Post date:** [January 16, 2025, 4:09pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427/4 "2025-01-16T16:09:30Z")

</div>

I also tried to convert the .txt files to .tsv.gz, and then rerun sc.read\_10\_mtx, but I get the following error:

```auto
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/core/indexes/base.py:3805, in Index.get_loc(self, key)
   3804 try:
-> 3805 return self._engine.get_loc(casted_key)
   3806 except KeyError as err:

File index.pyx:167, in pandas._libs.index.IndexEngine.get_loc()

File index.pyx:196, in pandas._libs.index.IndexEngine.get_loc()

File pandas/_libs/hashtable_class_helper.pxi:2606, in pandas._libs.hashtable.Int64HashTable.get_item()

File pandas/_libs/hashtable_class_helper.pxi:2630, in pandas._libs.hashtable.Int64HashTable.get_item()

KeyError: 1

The above exception was the direct cause of the following exception:

KeyError Traceback (most recent call last)
Cell In[13], line 1
----> 1 adata = sc.read_10x_mtx('/home/slacava3/data_jkebsch1/salvo/Xenopus_levis/code/GSE165371_cb_adult_mouse/', prefix = 'cb_adult_mouse_', cache_compression= 'gzip')

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/legacy_api_wrap/ __init__.py:82, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
     79 @wraps(fn)
     80 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
     81 if len(args_all) <= n_positional:
---> 82 return fn(*args_all, **kw)
     84 args_pos: P.args
     85 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/scanpy/readwrite.py:561, in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only, prefix)
    559 prefix = "" if prefix is None else prefix
    560 is_legacy = (path / f"{prefix}genes.tsv").is_file()
--> 561 adata = _read_10x_mtx(
    562 path,
    563 var_names=var_names,
    564 make_unique=make_unique,
    565 cache=cache,
    566 cache_compression=cache_compression,
    567 prefix=prefix,
    568 is_legacy=is_legacy,
    569 )
    570 if is_legacy or not gex_only:
    571 return adata

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/scanpy/readwrite.py:601, in _read_10x_mtx(path, var_names, make_unique, cache, cache_compression, prefix, is_legacy)
    595 genes = pd.read_csv(
    596 path / f"{prefix}{'genes' if is_legacy else 'features'}.tsv{suffix}",
    597 header=None,
    598 sep="\t",
    599 )
    600 if var_names == "gene_symbols":
--> 601 var_names_idx = pd.Index(genes[1].values)
    602 if make_unique:
    603 var_names_idx = anndata.utils.make_index_unique(var_names_idx)

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/core/frame.py:4102, in DataFrame. __getitem__ (self, key)
   4100 if self.columns.nlevels > 1:
   4101 return self._getitem_multilevel(key)
-> 4102 indexer = self.columns.get_loc(key)
   4103 if is_integer(indexer):
   4104 indexer = [indexer]

File ~/.conda/envs/MyEnv/lib/python3.11/site-packages/pandas/core/indexes/base.py:3812, in Index.get_loc(self, key)
   3807 if isinstance(casted_key, slice) or (
   3808 isinstance(casted_key, abc.Iterable)
   3809 and any(isinstance(x, slice) for x in casted_key)
   3810 ):
   3811 raise InvalidIndexError(key)
-> 3812 raise KeyError(key) from err
   3813 except TypeError:
   3814 # If we have a listlike key, _check_indexing_error will raise
   3815 # InvalidIndexError. Otherwise we fall through and re-raise
   3816 # the TypeError.
   3817 self._check_indexing_error(key)

KeyError: 1

```

---

<div class="post-metadata">

**Author:** ![gtca](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/gtca/32/1199_2.png) [@gtca](https://discourse.scverse.org/u/gtca)\
**Post date:** [January 17, 2025, 8:27pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427/5 "2025-01-17T20:27:46Z")

</div>

Hey @Slack90,

> where it should be .csv

The default format for the cell barcode and feature information files is `.tsv.gz` as specified [in the CellRanger documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-mex-matrices).

You can always read the `.mtx` file and metadata independently to construct an AnnData object with `AnnData(X=X, obs=cell_barcodes, var=features)`:

```py
from scipy.io import mmread
import pandas as pd

X = mmread("cb_adult_mouse.mtx")
cell_barcodes = pd.read_csv("cb_adult_mouse_barcodes.tsv.gz", compression="gzip", sep="\t")
features = pd.read_csv("cb_adult_mouse_genes.tsv.gz", compression="gzip", sep="\t")

```