Man pages for hclimente/martini
GWAS Incorporating Networks
| arrange_covars | Prepare covariates for 'scones' |
| calculateE | Calculate the environmental component of the phenotype |
| calculateG | Calculate the genetic component of the phenotype |
| check_installed | Check package is installed |
| connect_biomart | Open a biomaRt connection |
| get_adjacency | Compute Laplacian matrix |
| get_GI_network | Get gene-interaction network. |
| get_GM_network | Get gene membership network. |
| get_grid | Parse 'scones.cv' settings |
| get_GS_network | Get genomic sequence network |
| get_gxg | Get gene interactions |
| get_gxg_biogrid | Get BioGRID protein-protein interactions. |
| get_gxg_string | Get STRING protein-protein interactions. |
| get_snp_modules | Return groups of interconnected SNPs. |
| group_snps | Groups nearby SNPs |
| gwas2bed | Converts a MAP data.frame to a BED data.frame |
| is_coherent | Check inner coherence of GWAS dataset |
| ldweight_edges | Include linkage disequilibrium information in the network. |
| maxflow | Maxflow algorithm |
| mget_gxg_biogrid | Memoised version of get_gxg_biogrid |
| mget_gxg_string | Memoised version of get_gxg_stringdb |
| mincut | Run min-cut algorithm |
| mincut_c | Min-cut algorithm |
| mincut.cv | Run the cross-validated min-cut algorithm |
| minigwas | Description of the minigwas dataset. |
| minippi | PPIs for the minigwas dataset. |
| minisnpMapping | Genes for the minigwas dataset. |
| organism_id2name | Tax id to ensembl species name |
| permute_snpMatrix | Permute samples |
| plot_ideogram | Ideogram of SConES results. |
| sanitize_map | Check map |
| sanitize_snpMapping | Check snpMapping |
| scones | Find connected explanatory SNPs |
| scones_ | Find connected explanatory features |
| scones.cv | Find connected explanatory SNPs. |
| scones.cv_ | Find connected explanatory features |
| score_fold | Score the solutions of a k-fold |
| search_cones | Find connected explanatory SNPs. |
| sigmod | Find connected explanatory SNPs |
| sigmod_ | Find connected explanatory features |
| sigmod.cv | Find connected explanatory SNPs. |
| sigmod.cv_ | Find connected explanatory features |
| simulate_causal_snps | Simulate causal SNPs |
| simulate_phenotype | Simulate phenotype |
| snp2ensembl | Map SNPs to Ensembl genes. |
| snp_test | Calculate genotype-phhenotype associations |
| subnet | Subgraph of vertices with an attribute |
| subset_snpMatrix | Subsample snpMatrix |
| subvert | Vertices with an attribute |
| wrap_Xy | Make pseudo SnpMatrix object |
