Man pages for isglobal-brge/EpiMutations
Robust outlier identification for DNA methylation data
| add_ensemble_regulatory | Add ENSEMBL regulatory regions to epimutations |
| annotate_cpg | Annotate the DMR resulting from epimutacions package |
| annotate_epimutations | Annotate the results of epimutations or... |
| AS204 | Algorithm AS 204 |
| betas_from_bump | Obtains bumps beta values |
| betas_sd_mean | Computes beta values, standard deviation and mean to plot the... |
| cols_names | Sets common column names in a data frame |
| create_GRanges_class | Generates a GRanges object |
| epi_beta | Identifies epimutations based on a beta distribution. |
| epi_iForest | Identifies epimutations using Isolation Forest |
| epi_mahdist | Identifies epimutations using Robust Mahalanobis distance |
| epi_manova | Identifies epimutations using MANOVA |
| epi_mlm | Detects epimutations using Multivariate Linear Model (MLM) |
| epimutations | Epimutations analysis based on outlier detection methods |
| epimutations_one_leave_out | Epimutations analysis based on outlier detection methods |
| epi_parameters | Settings for parameters of 'epimutations' and... |
| epi_preprocess | Preprocess methylation array |
| epi_quantile | Identifies epimutations using quantile distribution |
| getBetaParams | Model methylation as a beta distribution |
| get_candRegsGR | Candidate regions to be epimutations |
| get_ENSEMBL_data | Get ENSEMBL regulatory features overlapping a genomic region |
| GRset | GRset |
| merge_records | Merge records for the same ENSEMBL regulatory element |
| mlm | Non-parametric, Asymptotic P-values for Multivariate Linear... |
| mlmtst | Sums of Squares and Pseudo-F Statistics from a Multivariate... |
| norm_parameters | Settings for parameters of epi_preprocess function |
| p.asympt | Asymptotic P-values |
| plot_epimutations | Plot a given epimutation and locate it along the genome |
| process_ENSEMBL_results | Process data from ENSEMBL |
| res.epi.manova | res.epi.manova |
| res_iForest | Creates a data frame containing the results obtained from... |
| res_mahdist | Creates a data frame containing the results obtained from... |
| res_manova | Creates a data frame containing the results obtained from... |
| res_mlm | Creates a data frame containing the results obtained from MLM |
| UCSC_annotation | UCSC gene annotations |
| UCSC_regulation | UCSC annotation |
