Package index

All functions

bb_mean()

Likelihood ratio test for mean allelic imbalance (per gene)

bb_var()

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.

calc_mad()

Calculating MAD^2 on the dispersion trend residuals

correct_theta()

Fits a local regression model with dispersion as a function of total gene counts. Predicted values are the expected dispersion for genes with similar expression levels The initial dispersion estimates are shrunk towards the trend

estim_bbparams()

Estimate beta-binomial distribution parameters per gene. The users can remove low abundant or low expressed genes through quality control parameters min_counts and min_cells.

estim_delta()

Estimating appropriate tuning paramaters delta and the number of degrees of freedom, N. We assume that dispersion follows Gamma distribution. Appropriate shrinkage is selected based on the MLE of the the difference between fitted dispersion and shrunk dispersion

geBoxplot()

Boxplot of allele-specific expression

glob_disp()

Estimates global beta-binomial distribution parameters on all genes together to evaluate the degree of skewness towards the reference allele. For the estimation, genes located on the sex chromosomes and imprinted genes are excluded

group_mean()

Performs test to detect changes in allelic ratio distribution across discrete groups.

group_var()

Performs test to detect changes in allelic ratio variation across descrete groups.

makedf()

preparing data frame for plotting

make_plotdf_simul()

posterior counts simulated under the expected dispersion

plot_disp()

Plot to visualize original and shrunk dispersion

plot_disp_fit_mean()

Plot to visualize allelic ratio modelled as a function of total gene counts

plot_disp_fit_theta()

Plot to visualize dispersion modelled as a function of total gene counts

plot_distr()

plotting allelic ratio distribution

plot_exp_disp()

plotting mean gene expression vs allelic dispersion

plot_glob_params()

Plot histogram of allelic ratio distribution across all genes with beta function based on alpha and beta global parameters

plot_MA()

Plotting distribution of allelic ratio over mean expression

plot_theta_density()

Density plot comparing allelic ratio distribution under observed and expected dispersion