Man pages for Alice-MacQueen/snpdiver
Explore SNP Effects on Multiple Phenotypes in Diversity Panels
| big_upset_df | Plot the -log10p-value distributions for two univariate GWAS... |
| check_covmat_basics | Basic sanity check for covariance matrices |
| check_positive_definite | check matrix for positive definitness |
| dive_effects2mash | Wrapper to run mash given a phenotype data frame |
| dive_phe2effects | Wrapper to run mash given a phenotype data frame |
| dive_phe2mash | Wrapper to run mash given a phenotype data frame |
| div_gwas | Wrapper for bigsnpr for GWAS |
| div_lambda_GC | Return lambda_GC for different numbers of PCs for GWAS on... |
| expand_cov | Create expanded list of covariance matrices expanded by grid,... |
| get_best_PC_df | Return best number of PCs in terms of lambda_GC |
| get_colnames | Get column names from a mash object |
| get_date_filename | Get current date-time in a filename-appropriate format. |
| get_estimated_pi | Return the estimated mixture proportions. Use... |
| get_GxE | Get data frames of types of GxE from a mash object |
| get_lambdagc | Find lambda_GC value for non-NA p-values |
| get_log10bf | Return the Bayes Factor for each effect |
| get_marker_df | Get mash marker_df |
| get_ncond | Get number of conditions |
| get_n_significant_conditions | Count number of conditions each effect is significant in |
| get_pairwise_sharing | Compute the proportion of (significant) signals shared by... |
| get_qqplot | Create a quantile-quantile plot with ggplot2. |
| get_significant_results | From a mash result, get effects that are significant in at... |
| get_top_results_clumped | Clump SNPs from a mash object based on -log10BF |
| get_U_by_mass | Get the positions of objects in a mash object Ulist that are... |
| labelled_stop | A wrapper function to 'stop' call |
| mash_plot_covar | ggplot of covariance matrix masses |
| mash_plot_manhattan_by_condition | Manhattan plot in ggplot colored by significant conditions |
| mash_plot_marker_effect | ggplot of single mash effect |
| mash_plot_pairwise_sharing | Create a ggplot of pairwise sharing of mash effects |
| mash_plot_sig_by_condition | Significant SNPs per number of conditions |
| mash_plot_Ulist | ggplot of specific covariance matrix patterns |
| pipe | Pipe operator |
| plot_qq_two_gwas | Plot the -log10p-value distributions for two univariate GWAS... |
| printf2 | print message function if verbose |
| reorder_cormat | Reorder correlation matrix |
| round2 | Return a number rounded to some number of digits |
| round_xy | Return a dataframe binned into 2-d bins by some x and y. |
| scale_cov | Scale each covariance matrix in list Ulist by a scalar in... |
| thresholdFBM | Threshold a FBM |
| tidyeval | Tidy eval helpers |
