geneSiteTable.base — geneSiteTable.base • Longcell

An interface function to apply geneSiteTable_df for target genes in a Splice object

Usage

geneSiteTable.base(
  spliceOb,
  gene_bed,
  genes = "all",
  eps = 0.05,
  bed_gene_col = "gene",
  bed_strand_col = "strand",
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

spliceOb: A Splice object
gene_bed: The gene bed annotation, should include the gene name and the gene strand.
genes: The target genes to generate meta sites, default for all genes
eps: The threshold for two sites to be merged
bed_gene_col: The name of the column to record the gene name in the gene bed
bed_strand_col: The name of the column to record the gene strand in the gene bed
overwrite: The flag to decide if overwrite the computed metaSite object
verbose: The flag to indicate if print the information

Value

A Splice object with meta sites stored the in the meta_sites slot.

Details

An interface function to apply geneSiteTable_df for target genes in a Splice object