segmentSeq-package | Segmentation of the genome based on multiple samples of high-throughput sequencing data. |
alignmentClass | Class "alignmentClass" |
alignmentClass-class | Class "alignmentClass" |
alignmentData | Class "alignmentData" |
alignmentData-class | Class "alignmentData" |
alignmentMeth | Class "alignmentMeth" |
alignmentMeth-class | Class "alignmentMeth" |
averageProfiles | Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions). |
cbind-method | Class "alignmentClass" |
cbind-method | Class "alignmentData" |
cbind-method | Class "alignmentMeth" |
classifySeg | A method for defining a genome segment map by an empirical Bayesian classification method |
dim-method | Class "alignmentClass" |
dim-method | Class "alignmentData" |
dim-method | Class "alignmentMeth" |
dim-method | Class "lociData" |
dim-method | Class "methData" |
dim-method | Class "segClass" |
dim-method | Class "segData" |
dim-method | Class "segMeth" |
findChunks | Identifies 'chunks' of data within a set of aligned reads. |
getCounts | Gets counts from alignment data from a set of genome segments. |
getOverlaps | Identifies overlaps between two sets of genomic coordinates |
heuristicSeg | A (fast) heuristic method for creation of a genome segment map. |
initialize-method | Class "alignmentClass" |
initialize-method | Class "alignmentData" |
initialize-method | Class "alignmentMeth" |
initialize-method | Class "segClass" |
initialize-method | Class "segData" |
initialize-method | Class "segMeth" |
lociData | Class "lociData" |
lociData-class | Class "lociData" |
lociLikelihoods | Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus. |
mergeMethSegs | Merges neighbouring methylation loci with the same pattern of expression. |
methData | Class "methData" |
methData-class | Class "methData" |
plotAverageProfile | Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions). |
plotGenome | Plots the alignment of sequence tags on the genome given an 'aligmentData' object and (optionally) a set of segments found. |
plotMeth | Plots a map of cytosine methylation (and optionally, methylation loci). |
plotMethDistribution | Plots the distribution of methylation on the genome. |
processAD | Processes an 'alignmentData' or 'alignmentMeth' object into a 'segData' or 'segMeth' object for segmentation. |
readBAM | Functions for processing files of various formats into an 'alignmentData' object. |
readGeneric | Functions for processing files of various formats into an 'alignmentData' object. |
readMeths | A function for reading data from the YAMA methylation aligner (or similarly parsed data) from which to identify methylation loci and/or differentially methylated regions. |
segClass | Class "segClass" |
segClass-class | Class "segClass" |
segData | Class "segData" |
segData-class | Class "segData" |
segmentSeq | Segmentation of the genome based on multiple samples of high-throughput sequencing data. |
segMeth | Class "segMeth" |
segMeth-class | Class "segMeth" |
selectLoci | Filters a 'lociData' object based on given selection criteria. |
show-method | Class "alignmentClass" |
show-method | Class "alignmentData" |
show-method | Class "alignmentMeth" |
show-method | Class "lociData" |
show-method | Class "methData" |
show-method | Class "segClass" |
show-method | Class "segData" |
show-method | Class "segMeth" |
SL10 | Example data selected from a set of Illumina sequencing experiments. |
SL26 | Example data selected from a set of Illumina sequencing experiments. |
SL32 | Example data selected from a set of Illumina sequencing experiments. |
SL9 | Example data selected from a set of Illumina sequencing experiments. |
summariseLoci | Summarise the expected number of loci in a 'lociData' object. |
[-method | Class "alignmentClass" |
[-method | Class "alignmentData" |
[-method | Class "alignmentMeth" |
[-method | Class "lociData" |
[-method | Class "methData" |
[-method | Class "segClass" |
[-method | Class "segData" |
[-method | Class "segMeth" |