Package index • scMultiMap

scMultiMap functions

Functions for inferring cell-type-specific peak-gene associations

scMultiMap(): scMultiMap

scMultiMap_WLS_by_gene(): WLS utility function.

scMultiMap_WLS(): Weighted least squares (WLS) in scMultiMap

scMultiMap_IRLS(): Iteratively reweighted least squares (IRLS) in scMultiMap

get_top_peak_gene_pairs(): get_top_peak_gene_pairs

Supporting toy data sets

Data sets for illustrative purposes

small_obj: A small pedagogical Seurat object

small_pairs_df: A data frame of peak-gene pairs, to be used with small_obj

small_irls_list: A toy example of estimated results from scMultiMap_IRLS() on small_obj.

example_pair: A simulated independent peak-gene pair

example_pair_bsample: A simulated perfectly correlated peak-gene pair with multiple biological samples present

Supporting helper functions

Helper functions for downstream analysis or handling peak data

make_gene_to_peak_link(): make_gene_to_peak_link

validate_with_assay(): validate_with_assay

CollapseToLongestTranscript(): CollapseToLongestTranscript

DistanceToTSS(): Find peaks near genes