Man pages for Alice-MacQueen/CDBNgenomics
Genomics Using the Cooperative Dry Bean Nursery Dataset
| anno_info | Annotation information |
| BLUPs | Best Linear Unbiased Predictors for 21 phenotypes from the... |
| cdbn_bigsnp2mashr | Convert bigsnpr output to mashr input dataframes. |
| cdbn_gwas | Wrapper for bigsnpr for GWAS on Phaseolus vulgaris (the... |
| cdbn_standard_gwas | Wrapper for my standard GWAS functions for the CDBN. |
| expand_cov | Create expanded list of covariance matrices expanded by grid,... |
| gapit_model_selection | Select the best number of PCs using BIC. |
| gapit_results_in_filepath | Identify trait names for GAPIT results. |
| get_annotations | Create a Table of Annotated Top SNPs for Phaseolus vulgaris |
| get_best_PC_df | Return best number of PCs in terms of lambda_GC for the CDBN. |
| 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_kinship | Find a kinship matrix using the van Raden method. |
| get_lambdagc | Find lambda_GC value for non-NA p-values |
| get_lambda_GC | Return lambda_GC for different numbers of PCs for GWAS on any... |
| 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_results_in_folder | Identify phenotype names from bigsnpr results in a folder. |
| get_significant_results | From a mash result, get effects that are significant in at... |
| get_SVD | Wrapper for the snp_autoSVD function for the CDBN. |
| get_top_effects_log10p | Step One of bigsnp2mashr |
| get_U_by_mass | Get the positions of objects in a mash object Ulist that are... |
| load_g2m_df | Read in the random and the strong datasets |
| mash_plot_covar | ggplot of covariance matrix masses |
| mash_plot_effects | ggplot of single mash effect |
| mash_plot_manhattan_by_condition | Manhattan plot in ggplot colored by significant conditions |
| 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 |
| mash_standard_run | A standard run of mashr |
| metadata | Metadata for 327 entries in the CDBN panel. |
| pipe | Pipe operator |
| Pv_GO | Phaseolus vulgaris gene ontology information |
| Pv_kegg | Phaseolus vulgaris kegg information |
| 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... |
| s_hat_bigsnp | Step Two of bigsnp2mashr |
| theme_oeco | Oeco ggplot theme |
| txdb | Annotation genomic ranges for Phaseolus vulgaris |
