Man pages for Alice-MacQueen/switchgrassGWAS
Genome Wide Association on Panicum virgatum
| anno_info | Annotation information from... |
| asv_best_PC_df | Return best number of PCs in terms of lambda_GC following... |
| dots | Set an advanced argument |
| 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 for Panicum... |
| 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_mash_metadata | Get switchgrass metadata for SNPs in a mash object. |
| 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_significant_results | From a mash result, get effects that are significant in at... |
| get_U_by_mass | Get the positions of objects in a mash object Ulist that are... |
| gff_gene | GFF3 Gene information |
| gff_metadata | Metadata lines for the gene GFF3 |
| load_mash_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 |
| mt.rawp2adjp | Adjusted p-values for simple multiple testing procedures |
| pipe | Pipe operator |
| pvdiv_autoSVD | Wrapper for the snp_autoSVD function for switchgrass. |
| pvdiv_bigsnp2mashr | Convert bigsnpr output to mashr input dataframes. |
| pvdiv_bigsnp2tibble | Convert A 'FBM.code256' SNP subset to a dataframe. |
| pvdiv_bigsnp_subset | Make a SNP dataframe subset from annotation table or a... |
| pvdiv_fbm_qq | Plot the -log10p-value distributions for two univariate GWAS... |
| pvdiv_fbm_upset_df | Plot the -log10p-value distributions for two univariate GWAS... |
| pvdiv_fdr | Compute Adjusted False Discovery Rate for pvdiv_gwas output. |
| pvdiv_gwas | Wrapper for bigsnpr for GWAS on Panicum virgatum. |
| pvdiv_kinship | Find a kinship matrix using the van Raden method. |
| pvdiv_lambda_GC | Return lambda_GC for different numbers of PCs for GWAS on... |
| pvdiv_manhattan | Create a Manhattan plot with ggplot2. |
| pvdiv_metadata | Metadata table for the Panicum virgatum diversity panel |
| pvdiv_phenotypes | Phenotypes available for the Panicum virgatum diversity... |
| pvdiv_qqplot | Create a quantile-quantile plot with ggplot2. |
| pvdiv_results_in_folder | Identify phenotype names from bigsnpr results in a folder. |
| pvdiv_standard_gwas | Juenger lab standard GWAS function. |
| pvdiv_subset_popgenome | Get GFF subsets |
| pvdiv_table_topsnps | Create a Table of Annotated Top SNPs for Panicum virgatum |
| pvdiv_top_effects_log10p | Step One of bigsnp2mashr |
| pvdiv_vcf_popgenome | Format the VCF subset |
| 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 |
| thresholdFBM | Threshold a FBM |
