decoupler.filter_by_expr

decoupler.filter_by_expr(adata, obs=None, group=None, lib_size=None, min_count=10, min_total_count=15, large_n=10, min_prop=0.7)

Determine which genes have sufficiently large counts to be retained in a statistical analysis.

Adapted from the function filterByExpr of edgeR (https://rdrr.io/bioc/edgeR/man/filterByExpr.html).

Parameters:

adataAnnData: AnnData obtained after running decoupler.get_pseudobulk.
obsDataFrame, None: If provided, metadata dataframe, only needed if adata is not an AnnData.
groupstr, None: Name of the .obs column to group by. If None, it assumes that all samples belong to one group.
lib_sizeint, float, None: Library size. If None, default to the sum of reads per sample.
min_countint: Minimum count requiered per gene for at least some samples.
min_total_countint: Minimum total count required per gene across all samples.
large_nint: Number of samples per group that is considered to be “large”.
min_propfloat: Minimum proportion of samples in the smallest group that express the gene.

Returns: