Man pages for andigoni/MeinteR
A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
| bed2Seq | Fetch sequences from bed-formatted data frames |
| cpgIslands | CpG islands (reference data) |
| cTF | Conserved transcription factors (reference data) |
| filterByCGI | Filter by CpG islands |
| filterByProm | Filter by promoters |
| findAltSplicing | Find alternative splicing events |
| findConservedTFBS | Find differentially methylated sites overlapping... |
| findPals | Find palindromes in a bed-formatted dataset |
| findQuads | Find quadruplexes in sequences centered at CpG sites |
| findShapes | Find putative conformational DNA changes |
| findSpliceSites | Find splice sites |
| findTFBS | Find putative transcription factor binding sites |
| importGEO | Import GEO data series in the workspace |
| importLimma | Imports the results of differential methylation analyses... |
| isEmptyDF | Check if data frame is empty |
| loadFile | Load input data |
| loadSeqGEO | Reformat methylation sequencing data fetched from GEO |
| meinter | Calculate the genomic index of methylation sites based on the... |
| nameStudy | Set a study name |
| plotBeta | Plot scores of the input data Generates a density plot of the... |
| plotCpG | Plot G+C-content and observed/expected ratio. |
| plotTF | Create barplot of the identified transcription factor binding... |
| refFreq | Human transcription factor frequency (reference data) |
| reorderBed | Reorder tabular methylation data to bed format |
| sample | Sample DNA methylation dataset (sample data) |
| scatterConsTF | Create a scatterplot of the identified conserved... |
| test.data | Test dataset with chromosomal position of the methylated... |
| TF.class | Transcription factor classes (reference data) |
| validateBed | Validate format of the input bed data |
