Man pages for segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing data
| alignmentClass-class | Class "alignmentClass" |
| alignmentData-class | Class "alignmentData" |
| alignmentMeth-class | Class "alignmentMeth" |
| averageMethylationRegions | Computes and plots the average distribution of aligned reads... |
| classifySeg | A method for defining a genome segment map by an empirical... |
| findChunks | Identifies 'chunks' of data within a set of aligned reads. |
| getCounts | Gets counts from alignment data from a set of genome... |
| getOverlaps | Identifies overlaps between two sets of genomic coordinates |
| givenExpression | Adjusts posterior likelihoods of differential expression by... |
| heuristicSeg | A (fast) heuristic method for creation of a genome segment... |
| hSL | Preprocessed 'lociData' object containing likelihoods of... |
| lociData-class | Class "lociData" |
| lociLikelihoods | Evaluates the posterior likelihoods of each region defined by... |
| mergeMethSegs | Merges neighbouring methylation loci with the same pattern of... |
| methData-class | Class "methData" |
| normaliseNC | A function providing adjustment of cytosine... |
| plotGenome | Plots the alignment of sequence tags on the genome given an... |
| plotMeth | Plots a map of cytosine methylation (and optionally,... |
| plotMethDistribution | Plots the distribution of methylation on the genome. |
| processAD | Processes an 'alignmentData' or 'alignmentMeth' object into a... |
| readMethods | Functions for processing files of various formats into an... |
| readMeths | A function for reading data from the YAMA methylation aligner... |
| segClass-class | Class "segClass" |
| segData-class | Class "segData" |
| segmentSeq-package | Segmentation of the genome based on multiple samples of... |
| segMeth-class | Class "segMeth" |
| selectLoci | Filters a 'lociData' object based on given selection... |
| SL | Example data selected from a set of Illumina sequencing... |
| summariseLoci | Summarise the expected number of loci in a 'lociData' object. |
| thresholdFinder | Determines threshold for the proportion of methylation at... |
