Generalized likelihood ratio test for a gene. — gene

an interface function to run GLRT for specified exons in a gene for specified two cell groups from a Splice object.

Usage

gene_GLRT.base(
  spliceOb,
  gene,
  group1,
  group2,
  exons = "all",
  iters = 100,
  psi_num = 500,
  group_cell_thresh = 30,
  verbose = FALSE,
  ...
)

Arguments

spliceOb: a Splice object
gene: the name of specified gene
group1: cells for group 1
group2: cells for group 2
exons: specified exons to do GLRT
iters: the number of iterations for bootstrap
psi_num: the sample size from two beta distributions to calculate the earth-moving distance
group_cell_thresh: the minimum cell number for each group for GLRT
verbose: whether to print out the iteration information
...: parameters specified for geneSiteTable()
gene_bed: a dataframe of gene bed annotation
gtf: a dataframe of gtf annotation
exon_len_thresh: the minimum length of exons for GLRT

Value

a dataframe of the test result. Each line is an exon with p-values and parameters for the psi distributions in two cell populations if they have significant difference