compute phi for exons in multi-genes — genesSitesPhi.base • Longcell

compute phi for exons in a gene from a Splice object

Usage

genesSitesPhi.base(
  spliceOb,
  genes,
  cells = "all",
  cell_count_thresh = 20,
  exprs_thresh = 10,
  iters = 100,
  psi_lwr = 0.1,
  psi_upr = 0.9,
  phi_conf_thresh = 0.2,
  method = match.arg("beta", "psi"),
  CI_level = 0.05,
  verbose = TRUE,
  ...
)

Arguments

spliceOb: the Splice object
cells: cells to use in building exon count table
cell_count_thresh: the minimum number of cells expressing this gene
exprs_thresh: the minimum gene expression to calculate the exon psi (for unbiased estimation)
iters: iteration for bootstrap to generate the confidence interval of phi
psi_lwr, psi_upr: The lower and upper bound to preserve as alternative spliced exons
phi_conf_thresh: The maximum length of confidence interval to filter out inconfident phi estimation
method: The method to use for phi estimation
CI_level: The alpha for the confidence interval of phi estimation
verbose: The flag to indeicate if the intermediate messages should be printed
...: Other parameters for geneSitesPsi.base

Value

a dataframe recording the phi estimation