cellink.tl.external.genescores_to_100kb_bedgraph

cellink.tl.external.genescores_to_100kb_bedgraph(genescores, gene_annotation, *, window_kb=100, gene_col='GENE', chr_col='CHR', start_col='START', end_col='END', use_bedtools_for_merge=True)

Convert gene scores to 100kb window bedgraphs.

For each gene with a non-zero score, creates a bedgraph interval spanning [TSS - window_kb, TES + window_kb]. The score is the gene’s probabilistic score (no activity weighting).

This is the secondary sc-linker S2G strategy, reported alongside the primary ABC_Road strategy.

Parameters:

• genescores (DataFrame) – DataFrame (genes X programs) with probabilistic scores in [0, 1].

• gene_annotation (DataFrame) – Gene coordinate DataFrame from load_gene_annotation.

• window_kb (int (default: 100)) – Window size in kilobases around gene body (default 100).

• gene_col (str (default: 'GENE')) – Column names in gene_annotation.

• chr_col (str (default: 'CHR')) – Column names in gene_annotation.

• start_col (str (default: 'START')) – Column names in gene_annotation.

• end_col (str (default: 'END')) – Column names in gene_annotation.

• use_bedtools_for_merge (bool (default: True)) – If True and bedtools available, use bedtools merge.

Return type:

dict[str, DataFrame]

Returns:

dict Program name → bedgraph DataFrame (chr, start, end, score).