Inference Tools

This module provides a comprehensive collection of tools tailored for the analysis and inference of isomatrix anndata objects. These tools facilitate the extraction of meaningful insights from complex datasets, enabling advanced data interpretation in the context of single cell resoloution isoform studies.

isoform_anndata_from_long_reads = sc.read_h5ad("/data/analysis/data_mcandrew/000-sclr-discovair/discovair_long_read_transcript_matrix_annotated.h5ad")

isoform_anndata_from_long_reads.X

array([[1., 0., 0., ..., 0., 0., 0.],
       [1., 1., 2., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       ...,
       [3., 0., 0., ..., 0., 0., 0.],
       [1., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.]], dtype=float32)

---

source

get_gene_mat

 get_gene_mat (adata, gene_column_name='geneId')

gene_matrix = get_gene_mat(isoform_anndata_from_long_reads)

---

source

get_iso_prop

 get_iso_prop (adata, gene_column_name)

isoform_anndata_from_long_reads.obsm["isoform_proportions"] = get_iso_prop(isoform_anndata_from_long_reads, gene_column_name='geneId')