compute_similarity_grammar_flat: compute_similarity_grammar_flat

In ThomasDCY/AdaLiftOver: Adaptive liftOver

compute_similarity_grammar_flat

Description

This function computes the sequence grammar similarities between query regions and the corresponding target regions.

Usage

compute_similarity_grammar_flat(
  gr_query,
  gr_target,
  query_genome,
  target_genome,
  motif_list,
  grammar_size = 500L,
  metric = "cosine"
)

Arguments

gr_query	The query genomic regions of GRanges class.
gr_target	The target genomic regions of GRanges class. The length of gr_target should be the same as the length of gr_query
query_genome	The query genome build identifier (e.g. 'mm10', 'hg38'). Make sure the corresponding BSgenome package is installed. Or a BSgenome class.
target_genome	The target genome build identifier (e.g. 'mm10', 'hg38'). Make sure the corresponding BSgenome package is installed. Or a BSgenome class.
motif_list	PWMatrixList, or PFMatrixList.
grammar_size	The nearby region (bp) to extract regulatory grammars. Default is 500L.
metric	The metric for computing similarities between indicators. One of 'cosine' and 'jaccard'. Default is 'cosine'.

Value

A numeric vector with values between 0 and 1.

Author(s)

Chenyang Dong [e-mail]

Examples

data('data_example')
data('jaspar_pfm_list')
similarity <- compute_similarity_grammar_flat(gr[2], gr_list[[2]], 'mm10', 'hg38', jaspar_pfm_list)

ThomasDCY/AdaLiftOver documentation built on June 2, 2025, 12:35 p.m.