Test to evaluate deviation from the expected level of allelic variation for genes with similar expression. Performs a permutation test between H_0: gene's dispersion is the same as the common (expected) dispersion. H_1: The stabilized (shrunk) dispersion is not the same as the common dispersion.
bb_var.RdTest to evaluate deviation from the expected level of allelic variation for genes with similar expression. Performs a permutation test between H_0: gene's dispersion is the same as the common (expected) dispersion. H_1: The stabilized (shrunk) dispersion is not the same as the common dispersion.
Usage
bb_var(
a1_counts,
tot_counts,
estimates,
estimates_group = NULL,
min_cells = 5,
min_counts = 5,
batch = NULL,
metadata = NULL,
n_pmt = 500,
n_sim = 500
)Arguments
- a1_counts
Integer matrix (genes x cells): allele-1 counts.
- tot_counts
Integer matrix (genes x cells): total counts (same dimenstions and rownames as
a1_counts).- estimates
Data frame from
correct_theta()- estimates_group
Optional object containing initial beta-binomial parameter estimates and correction performed on each batch separately
- min_cells
Integer >= 1. Minimum number of cells per gene to fit (default 5). Genes with a number of cells less than min_cells are excluded from the estimation.
- min_counts
Integer >= 0. Minimum reads per cell to include (default 0). Cells with a number of mapped reads less than min_counts are excluded from the estimation
- batch
Optional string: column name in
metadataidentifying batches. (if batch correction is required)- metadata
Optional metadata object containing cell level information (batch identifier must be one of the column in the cell metadata)
- n_pmt
Integer. Number of permutations (<= n_sim.)
- n_sim
Integer. Number of simulated replicates.