scglue.genomics.cis_regulatory_ranking

scglue.genomics.cis_regulatory_ranking(gene2region, region2tf, genes, regions, tfs, region_lens=None, n_samples=1000, random_state=None)

Generate cis-regulatory ranking between genes and transcription factors

参数:

• gene2region (Graph) – A graph connecting genes to cis-regulatory regions

• region2tf (Graph) – A graph connecting cis-regulatory regions to transcription factors

• genes (typing.List[str]) – A list of genes

• tfs (typing.List[str]) – A list of transcription factors

• regions (typing.List[str]) – A list of cis-regulatory regions

• region_lens (typing.Optional[typing.List[int]]) – Lengths of cis-regulatory regions (if not provided, it is assumed that all regions have the same length)

• n_samples (int) – Number of random samples used to evaluate regulatory enrichment (setting this to 0 disables enrichment evaluation)

• random_state (typing.Union[RandomState, int, None]) – 随机状态

返回类型:

DataFrame

返回:

gene2tf_rank – Cis regulatory ranking between genes and transcription factors