Man pages for llrs/integration-helper
Facilitate the integration
| access_reactome | Return data from reactome |
| allComb | Logical vectors of meta data |
| analyze | Analyze a sgcca object |
| angle | Calculates the angle between to slopes |
| aves | Method to simplify AVE |
| biological_relationships | Performs the calculation of biological information |
| boot_evaluate | Evaluates the bootstrapping of RGCCA |
| boots_corr | Bootstrapping to asses how probable is to have such... |
| boot_sgcca | Bootstrap sgcca |
| check_design | Validate designs |
| circle | A circle of radium 2 |
| circleFun | Create a circle |
| clean_unvariable | Remove unvariable features |
| colors | Useful colors |
| comb_prevalence | Look for prevalence in combinations of two |
| comp | Analyze the data for the relationship in time |
| compare | Compares two objects of class sgcca |
| compare.correlations | Calculates the z-score of two correlations |
| contingency_taxa | Compares the taxonomy of the otus |
| convert.z.score | Z-score to p-value |
| correct | Check that the network is fully connected |
| cor_sign | Significative correlation |
| cors_rgcca | Check the efficacy of RGCCA |
| dist2d | Calculate the distance between a line and a point |
| ensembl2symbol | Translate ensmbl to symbols |
| epitheliumE | Function to read the epithelium signature |
| fastercheck | Check if a vector is in the matrix |
| filter_RNAseq | Filter expressions |
| filter_values | Filter correlations |
| full_prevalence | Look for prevalence of a factor |
| getAVEs | Retrieve inner AVE |
| improve.sgcca | Improve the information on sgcca classes |
| integration | Integrate |
| Integration-package | Integrates data |
| intercorrelation | Intracorrelation |
| kFolding | Indexes for K-folds |
| loo_functions | Function to export a function |
| looIndex | Indexes without one sample |
| makeRects | Make a rectangle at those cells |
| McKeonHomeogenity | Calculates McKeon Homeogenity |
| meta_i_norm | Normalize 16S biopsies metadata |
| meta_r_norm | Normalize the metadata of the RNA |
| meta_s_norm | Normalize 16S stools metadata |
| model_columns | Adapt data for a CCA |
| model_RGCCA | Prepare data for CCA. |
| m_sem | Summarize a model |
| norm_expr_colnames | Change names of expression |
| norm_otus | Normalize OTUS |
| norm_RNAseq | Normalize RNAseq |
| pathsPerMicro | Enrichment by microorganisms |
| permanova_expr | Permanova |
| permanova_otus | Permanova |
| plotAVEs | Distribution of inner AVE |
| plot_cor | Plot a correlation with ggplot |
| plot_interesting | Plot PCA of interesting variables |
| plot_samples | Plot samples |
| plot_single_cor | Plot correlations |
| plot_variables | Plot bullseye |
| prevalence | Test prevalence |
| prevalence_tab | Calculates the presence or absence of a microorganism |
| probability_samples | Calculates the probability of obtaining these samples. |
| pvalue | Calculates the p.value |
| ratio | Ratio of prevalence |
| readSGCCA | Read component |
| relevant | List the correlations |
| select_genes_int | Filter genes |
| select_var | Select important variables |
| selectVar | Select variable from bootstrapping |
| sem | Standard error of the mean |
| sign_cor | List the correlations |
| size | Number of samples |
| store_micro | Store result by microorganism |
| subsetData | Subset a list |
| subSymm | Substitute in a symmetric matrix |
| symm | Create symmetric matrix |
| taxonomy | Clean and prepare the data from IMNGS |
| tidyer | Clean the output of a sgcca object |
| tol21rainbow | Rainbow colors |
| trimVer | Trim version number of genes |
| two.sided | Two sided test |
| variables | Extract in a tidy way the information about the variables |
| variables_weight | Plot density of the weight of components |
| weight_design | Check a design for different weights |
| weights | Select the weights and adds information for human RNAseq |
| weights_bayes | Independence between genes and OTUs |
| weights_correlation | Correlation weights |
| weights_otus | Select the weights and adds information for taxa RNAseq |
| wilks_rgcca | Check the efficacy of RGCCA |
| write_cor | Translate symbols and store |
