Man pages for simingz/ctwas
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits
| 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 | Converts PLINK genotype data to LD matrices and SNP info... |
| 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 |
| get_cs_correlation | Get correlations between CS, using variable with maximum PIP... |
| harmonize_wgt_ld | Harmonize z scores from GWAS to match ld reference genotypes.... |
| harmonize_z_ld | Harmonize z scores from GWAS to match ld reference genotypes.... |
| 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... |
| 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 |
| single_effect_regression | Bayesian single-effect linear regression |
| susie | Sum of Single Effects (SuSiE) Regression |
| susie_get_methods | Inferences From Fitted SuSiE Model |
| susieI | Iteratively run susie and estimate parameters |
| susie_init_coef | Initialize a susie object using regression coefficients |
| susieI_rss | Iteratively run susie and estimate parameters - RSS version |
| susie_rss | Sum of Single Effects (SuSiE) Regression using summary... |
| univariate_regression | Perform Univariate Linear Regression Separately for Columns... |
| write_ld_Rf | combine variant information associated with a LD R matrix... |
