Function reference • ctwas

All functions
`anno_susie()`	annotate susie results. this will generate output text files
`coef(<susie>)`	Extract regression coefficients from susie fit
`compute_ss()`	Compute sufficient statistics for susie.
`convert_geno_to_LD_matrix()`	Convert PLINK genotype data to LD matrices and SNP info files, save LD matrices as .RDS files and SNP info as .Rvar files
`ctwas()`	Causal inference for TWAS
`ctwas_locus_plot()`	Plot the output of cTWAS at a single locus
`ctwas_locus_plot_genetrack()`	Create the gene track for the cTWAS locus plot
`ctwas_rss()`	Causal inference for TWAS using summary statistics
`ctwas_summarize_parameters()`	Summarize and plot cTWAS parameter estimates
`filter_regions()`	filter regions based on probality of at most 1 causal effect
`harmonize_wgt_ld()`	Harmonize z scores from GWAS to match ld reference genotypes. Flip signs when reverse complement matches, remove/recover strand ambiguous SNPs
`harmonize_z_ld()`	Harmonize z scores from GWAS to match ld reference genotypes. Flip signs when reverse complement matches.
`impute_expr()`	Impute expression
`impute_expr_z()`	Impute expression z scores
`index_regions()`	Get gene and SNP index for each region
`predict(<susie>)`	Predict outcomes or extract coefficients from susie fit.
`preharmonize_z_ld()`	Harmonize GWAS summary statistics and LD reference
`prep_exprvar()`	Prepare .exprvar file
`prep_pgen()`	Read .pgen file into R
`prep_pvar()`	Prepare .pvar file
`read_bim()`	Read .bim file into R
`read_expr()`	Read .expr file into R
`read_exprvar()`	Read .exprvar file into R
`read_ld_Rvar()`	read variant information for all ld matrices in `ld_Rf`.
`read_ld_Rvar_RDS()`	read variant information associated with a LD R matrix .RDS file.
`read_pgen()`	Read pgen file into R
`read_pvar()`	Read .pvar file into R
`read_var_info()`	Read variant information from .pvar or .bim file into R
`region2core()`	parallel regions
`susie()` `susie_suff_stat()`	Sum of Single Effects (SuSiE) Regression
`susieI()`	Iteratively run susie and estimate parameters
`susieI_rss()`	Iteratively run susie and estimate parameters - RSS version
`susie_get_objective()` `susie_get_posterior_mean()` `susie_get_posterior_sd()` `susie_get_niter()` `susie_get_prior_variance()` `susie_get_residual_variance()` `susie_get_lfsr()` `susie_get_posterior_samples()` `susie_get_cs()` `susie_get_pip()`	Inferences From Fitted SuSiE Model
`susie_init_coef()`	Initialize a susie object using regression coefficients
`susie_rss()`	Sum of Single Effects (SuSiE) Regression using summary statistics
`univariate_regression()`	Perform Univariate Linear Regression Separately for Columns of X
`write_ld_Rf()`	combine variant information associated with a LD R matrix .RDS file.

Reference

All functions