segmentSeq-package |
Segmentation of the genome based on multiple samples of high-throughput sequencing data. |
alignmentData |
Class "alignmentData" |
alignmentData-class |
Class "alignmentData" |
cbind |
Class "alignmentData" |
cbind-method |
Class "alignmentData" |
classifySeg |
A method for defining a genome segment map by an empirical Bayesian classification method |
dim-method |
Class "alignmentData" |
dim-method |
baySeq - classes |
dim-method |
Class "segData" |
filterSegments |
Filters an set of segments (given an ordering on the segments) such that no segments overlap. |
findChunks |
Identifies 'chunks' of data within an 'alignmentData' object. |
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 "alignmentData" |
initialize-method |
Class "segData" |
lociLikelihoods |
Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus. |
mergeSD |
Merges multiple 'segData' objects. |
plotGenome |
Plots the alignment of sequence tags on the genome given an 'aligmentData' object and (optionally) a set of segments found. |
postSeg |
baySeq - classes |
postSeg-class |
baySeq - classes |
processAD |
Processes an 'alignmentData' object into a 'segData' object for segmentation. |
processTags |
Convenience function for processing tab-delimited files in a certain format into an 'alignmentData' object. |
segData-class |
Class "segData" |
segmentSeq |
Segmentation of the genome based on multiple samples of high-throughput sequencing data. |
show-method |
Class "alignmentData" |
show-method |
baySeq - classes |
show-method |
Class "segData" |
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. |
[-method |
Class "alignmentData" |
[-method |
baySeq - classes |
[-method |
Class "segData" |