Function reference • digitaltwins

Digital Twin Test Functions for running versions of the DTT. These functions are the core external-facing functions of this package.
`linear_crt()`	DTT using a fixed linear statistic
`linear_crt_indep()`	DTT with independence, using a fixed linear statistic
`conditional_tdt()`	The DTT with a TDT-like test statistic
Misc Other Functions Functions for processing DTT p-values, creating a synthetic population, and running the usual TDT.
`accum_test()`	Accumulation test with the hinge-exponential function
`generate_offspring()`	Generate a synthetic offspring
`haps_to_gen()`	Convert haplotype matrix to genotype matrix
`tdt()`	Computes TDT p-value
Data Sets Sample data sets.
`haps_matrix`	3,000 synthetic haplotypes from one chromosome
Internal functions These functions are intended only for internal use.
`col_cors()`	Correlation across columns
`create_offspring_population()`	Simulate an offspring population
`deviance_test_stats()`	Computed test statistics based on deviance change for GLM
`find_mate_pair()`	Find a pair of haplotypes.
`forward_backward_()`	forward_backward_
`gen_id_to_haps()`	Convert genotype IDs to haplotype IDs
`generate_ancestry()`	Generate ancestry information
`get_beta_glmnet()`	Run CV glmnet
`get_fb_results()`	Forward-backward algorithm for parent-offspring trio of haplotypes
`get_genotype_ids()`	Complete haplotype list
`get_phased_ancestry()`	Indentify maternal vs paternal haplotypes
`haps_id_to_gen()`	Convert haplotype IDs to genptype IDs
`hinge_exp()`	Hinge-exponential function
`impute_variant_fast()`	Imputes a set of variants
`logistic_ll()`	Logistic-log likelihood
`sample_ancestry_()`	sample_ancestry_
`sample_parity_poisson()`	Sample poisson conditional on its parity

Reference

Digital Twin Test

Misc Other Functions

Data Sets

Internal functions

Contents