Man pages for pbastide/phylolimma
Phylogenetic Comparative Methods for limma
| addReplicatesOnTree | Add replicates to a tree |
| checkParamMatrix | Check Matrix Parameter |
| classifyTestsF | Multiple Testing Across Genes and Contrasts |
| compute_inv_hessian | Get Inverse Hessian |
| ddf_samples | Function for vanilla ddf |
| ddf_satterthwaite | Function for Satterthwaite ddf |
| ddf_satterthwaite_BM_error | Satterthwaite for BM with error |
| ddf_satterthwaite_BM_error_approx | Satterthwaite for BM with error |
| ddf_species | Function for species ddf |
| decideTests | Multiple Testing Across Genes and Contrasts |
| dots | Capture dot arguments |
| eBayes | Empirical Bayes Statistics for Differential Expression |
| getBoundsSelectionStrength | Get Bounds on alpha |
| get_chol_tree | Get Tree Normalizing Inverse Cholesky |
| get_consensus_tree | Get transformed tree |
| get_consensus_tree_BM | Get BM transformed tree |
| get_consensus_tree_delta | Get delta transformed tree |
| get_consensus_tree_lambda | Get lambda transformed tree |
| get_consensus_tree_OUfixedRoot | Get OU transformed tree |
| get_consensus_tree_OUrandomRoot | Get OU transformed tree |
| get_C_tree | Get Tree Normalizing Inverse Cholesky |
| get_ddf | Get ddf function |
| get_dots_args | Get all paramters but lower and upper bounds and starting... |
| get_lambda_error | Get lambda value |
| get_lower_bounds | Get lower bounds on parameters |
| getMaxLambda | Get Max on lambda |
| getMinError | Get Min on sigma2_error |
| getSpeciesNumber | Get the number of species |
| get_starting_values | Get starting values on parameters |
| get_upper_bounds | Get upper bounds on parameters |
| hessianMinusLogLik | Hessian of the minus likelihood |
| lengthNormalizeRNASeq | Normalize RNASeq count data using gene lengths |
| lmFitLimma | Fit using limma |
| normalize_none | Normalize RNASeq count data |
| normalize_RPKM | Normalize RNASeq count data |
| normalize_TPM | Normalize RNASeq count data |
| parse_species | Add replicates to a tree |
| phylogeneticCorrelations | Phylogenetic COmparative Method using LIMMA |
| phylolimma-package | TODO |
| phylolmFit | Phylogenetic COmparative Method using LIMMA |
| PhyloMArrayLM-class | Class PhyloMArrayLM |
| pos_inv | Generalized positive inverse |
| rescale_tree | Scale tree to unit height |
| rho_prime | Compute 1 - rho |
| rho_prime_inv | Compute alpha from rhoprime |
| transform_data_tree | Transform data matrix |
| transform_design_tree | Transform design matrix |
| transform_tree_model_BM | Get BM transformed tree |
| transform_tree_model_delta | Get delta transformed tree |
| transform_tree_model_lambda | Get lambda transformed tree |
| transform_tree_model_OUfixedRoot | Get OU transformed tree |
| transform_tree_model_OUrandomRoot | Get OU transformed tree |
| transform_tree_phylolm | Get transformed tree |
| tree_height | Get maximum tree height |
