Man pages for Mathelab/ALTRE
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
| ALTRE | Workflow: Post-alignment to altered TSS-proximal and... |
| categAltrePeaks | Categorize altered peaks as experiment-specific,... |
| combineAnnotatePeaks | Combine and annotate peaks from different sample types.... |
| comparePeaksAltre | Comparison of methods for identifying altered regulatory... |
| countanalysis | Determines which regulatory regions are signifigantly altered... |
| getConsensusPeaks | Given a GRangeslist object with peaks for each samples,... |
| getCounts | Generates count data for regulatory regions. This function is... |
| getCountsFast | THIS FUNCTION FOR USE WHEN RUNNING ALTRE ON MACOS/LINUX ONLY!... |
| getTSS | get TSS file for use in combineAnnotatePeaks function. The... |
| grangestodataframe | Internal function: converts granges to dataframe |
| loadBamFiles | Read in BAM files (internal function) |
| loadBedFiles | Read in BED Files |
| loadCSVFile | Read in CSV file |
| mergeclosepeaks | Internal function: merges peaks within user input distance of... |
| plotCombineAnnotatePeaks | Given the output from combineAnnotatePeaks, plot a barplot... |
| plotCompareMethods | Plots a pie that compares altered regions as determined by... |
| plotCompareMethodsAll | Plots pie charts for comparison of two methods of identifying... |
| plotConsensusPeaks | Given the output from getConsensusPeaks, generate a barplot... |
| plotCountAnalysis | Create a volcano plot from the output of categAltrePeaks |
| plotDistCountAnalysis | Creates a boxplot to see the distribution of read counts in... |
| plotGetCounts | Given the output from getCounts, plot a density plot of log2... |
| plotGREATenrich | Given the output from processPathways(), creates a heatmap... |
| processPathways | Enrichment analysis using GREAT package to identify putative... |
| runGREAT | Enrichment analysis using GREAT package to identify putative... |
| runShinyApp | run shiny app |
| statscombineannotate | Internal function: creates a stat matrix for combined and... |
| tssannotgrange | Internal function: annotates peaks as TSS-proximals or... |
| writeBedFile | Creates a custom track for visualization on genome browser |
| writeCompareRE | Writes a data table generated by comparePeaksAltre |
| writeConsensusRE | Writes annotated genomic regions |
| writeGREATpath | Writes a data generated by pathenrich |
