snapatac2.tl.aggregate_X#
- snapatac2.tl.aggregate_X(adata, groupby=None, normalize=None, file=None)[source]#
Aggregate values in adata.X in a row-wise fashion.
Aggregate values in adata.X in a row-wise fashion. This is used to compute RPKM or RPM values stratified by user-provided groupings.
- Parameters:
adata (
AnnData
|AnnDataSet
) – The AnnData or AnnDataSet object.groupby (
str
|list
[str
] |None
) – Group the cells into different groups. If astr
, groups are obtained from.obs[groupby]
.normalize (
Optional
[Literal
['RPM'
,'RPKM'
]]) – normalization method: “RPM” or “RPKM”.file (
Path
|None
) – if provided, the results will be saved to a new h5ad file.
- Returns:
If
grouby
isNone
, return a 1d array. Otherwise, return an AnnData object.- Return type:
np.ndarray | AnnData