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. |
givenExpression |
Adjusts posterior likelihoods of differential expression by the likelihood that a locus is expressed. |
heuristicSeg |
A (fast) heuristic method for creation of a genome segment map. |
hSL |
Preprocessed 'lociData' object containing likelihoods of methylation at each locus. |
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" |
normaliseNC |
A function providing adjustment of cytosine methylated/unmethylated counts based on a nonconversion rate. |
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. |
thresholdFinder |
Determines threshold for the proportion of methylation at which a methylation locus may be identified. |
[-method |
Class "alignmentClass" |
[-method |
Class "alignmentData" |
[-method |
Class "alignmentMeth" |
[-method |
Class "lociData" |
[-method |
Class "methData" |
[-method |
Class "segClass" |
[-method |
Class "segData" |
[-method |
Class "segMeth" |