Man pages for explodecomputer/simulateGP
Functions for Simulating Genotype-Phenotype Relationships
| add_u | Add confounder variables and their instruments |
| allele_frequency | Estimate allele frequency from SNP |
| arbitrary_map | Create an arbitrary map |
| ascertain_samples | Ascertain some proportion of cases and controls from binary... |
| choose_effects | Get vector of effects that explain some amount of variance |
| contingency | Obtain 2x2 contingency table from marginal parameters and... |
| correlated_binomial | Simulate two correlated binomial variables |
| create_system | Wrapper for simulation pipeline |
| estimate_system_effects | Estimate the effects of all SNPs on all phenotypes |
| expected_mse | Calculate expected MSE |
| expected_se | Expected se given beta, af, n and vy |
| expected_ssx | Calculate expected SSX |
| fast_assoc | Get summary statistics in simple linear regression |
| generate_gwas_params | Generate SNP effects given MAF, h2 and selection |
| generate_gwas_ss | Modify SNP effects to account for LD |
| generate_gwas_ss_1 | Create a GWAS summary dataset |
| generate_ldobj | Generate LD matrix objects from reference panel |
| get_effs | Get effs for two traits and make dat format |
| get_ld | Get LD matrix for a specified region from bfile reference... |
| get_population_allele_frequency | Estimate the allele frequency in population from case/control... |
| get_regions_from_ldobjdir | Determine regions from LD file |
| gwas | Perform association of many SNPs against phenotype |
| gx_to_gp | Translate risk from liability to probability scale |
| hap_freqs | Estimate haplotype frequencies for two loci |
| init_parameters | Choose initial parameters for direct effects on X and Y |
| ldetect | Data frame of independent LD regions |
| lor_to_rsq | Estimate proportion of variance of liability explained by SNP... |
| make_geno | Create genotype matrix |
| make_mvdat | Take several exposures and one outcome and make the data... |
| make_phen | Simulate variable based on the influences of other variables |
| merge_exp_out | Organise outputs from 'gwas' into harmonised dat format |
| pipe | Pipe operator |
| range01 | Scale variable to have range between 0 and 1 |
| read_ldobjdir | Read in LD objects into list |
| recode_dat | Recode data to make every effect on x positive |
| recode_dat_intercept | Intercept recoding to have every effect on x positive |
| recode_dat_simple | Simple recoding to have every effect on x positive |
| risk_cross_plot | Plot liability vs probability disease risk |
| risk_simulation | Make simulation to compare disease and liability scales |
| sample_beta | Sample beta values given standard errors |
| sample_system_effects | Sample the actual effects based on initial parameters |
| simulate_geno | Simulate genotypes from haplotypes |
| simulateGP-package | simulateGP: Functions for Simulating Genotype-Phenotype... |
| simulate_haplotypes | Simulate haplotypes of two loci |
| simulate_population | Simulate individual level data from initial parameters |
| stuff | General funcs |
| summary_set | Wrapper for generating a summary set |
| test_ldobj | Create test LD object |
| test_system | Apply MR tests to system |
| y_to_binary | Convert continuous trait to binary |
