Generalized likelihood ratio test for multiples gene. — genes_groups

an interface function to run GLRT for all exons in multiple genes for multiple cell group pairs from a Splice object.

Usage

genes_groups_GLRT.base(
  spliceOb,
  genes,
  group1s,
  group2s,
  iters = 100,
  psi_num = 500,
  group_cell_thresh = 30,
  q_thresh = 0.05,
  filter = TRUE,
  verbose = FALSE,
  ...
)

Arguments

spliceOb: a Splice object
genes: a vector of gene names to do GLRT
group1s: a named list of cell names, each element should be cells belonging to a group
group2s: a named list of cell names, each element should be cells belonging to a group
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
q_thresh: the threshold for q value by fdr control
verbose: if print the process information
...: other parameters for gene_GLRT.base
cores: The number of cores used for parallization

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