All functions

anno_susie()

annotate susie results. this will generate out put txt files

coef(<susie>)

Extract regression coefficients from susie fit

compute_ss()

Compute sufficient statistics for susie.

ctwas()

Causal inference for TWAS

ctwas_rss()

Causal inference for TWAS using summary statistics

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 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

index_regions()

Get gene and SNP index for each region

predict(<susie>)

Predict outcomes or extract coefficients from susie fit.

prep_exprvar()

Prepare .exprvar file

prep_pgen()

Read .pgen file into R

prep_pvar()

Prepare .pvar file

read_expr()

Read .expr file into R

read_exprvar()

Read .exprvar file into R

read_ld_Rvar()

read variant information for all ld mattrices 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

region2core()

parallel regions

susie() susie_suff_stat()

Sum of Single Effects (SuSiE) Regression

susieI()

SuSiE iteraitve

susieI_rss()

SuSiE iteraitve 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