Man pages for jeffreyat/M2EFM
M2EFM
| build_m2efm | Build the M2EFM model. |
| evaluate | Calculates prognostic statistics based on m2eQTLs. |
| ExpressionData | ExpressionData |
| get_entrez_ids | Takes a vector of gene symbols and converts them to entrez... |
| get_gene_locs | Takes a data.frame with entrez ids and gene symbols and... |
| get_genes | Returns the genes to use from m2eQTL analysis. |
| get_m2eqtls | Finds m2eQTLs from gene expression and DNA methylation data. |
| get_pam50 | Get pam50 rorS scores for sample with gene expression data.... |
| get_probe_locs | Takes a vector of methylation probe ids and builds a table of... |
| get_probes | Returns the probes to use from m2eQTL analysis. |
| get_random_genes | Returns the genes to use selected at random. |
| load_exp | Takes the path to a gene expression matrix and return an... |
| load_it | load_it |
| load_meth | Takes the path to a DNA methylation matrix and return a... |
| mad_filter | Takes an ExpressionData object and filters it by the given... |
| MethylationData | MethylationData |
| MethylationData450k | MethylationData450k |
| mm | Display a message to the user. |
| plot.M2EFM_evaluation | Create boxplots of the evaluation results. |
| predict.M2EFM_models | Predict the M2EFM model on new data. |
| ProfileData | ProfileData |
| reduce_stage | Converts AJCC stages to a simple four stage form. |
| scale_samples | Scales individual samples to another dataset. |
| scale_values | Center and scale the expression values. |
| summary.M2EFM_evaluation | Summarize the results of an M2EFM evaluation. |
| summary.M2EFM_models | Summarize the results of an M2EFM models. |
