readMethods
(Package: segmentSeq) :
Functions for processing files of various formats into an `alignmentData' object.
These functions take alignment files of various formats to produce an object (see Details) describing the alignment of sequencing tags from different libraries. At present, BAM and text files are supported.
This function takes as input a set of files that describe the number of times a set of cytosines are observed to be methylated or unmethylated in some high-throughput sequencing data. It merges the data from these files into an object of 'alignmentMeth' class which can then be further processed to identify methylation loci.
The segData class inherits from the segClass class and contains data about potential segments on the genome, together with counts for each of those segments.
The segMeth class inherits from the segClass class and contains data about potential segments on the genome, together with counts for each of those segments.
The segmentSeq package is intended to take multiple samples of high-throughput data (together with replicate information) and identify regions of the genome which have a (reproducibly) high density of tags aligning to them. The package was developed for use in identifying small RNA precursors from small RNA sequencing data, but may also be useful in some mRNA-Seq and chIP-Seq applications.
The alignmentData class inherits from the alignmentClass class and records information about a set of alignments of high-throughput sequencing data to a genome. Details include the alignments themselves, the chromosomes of the genome to which the data are aligned, and counts of the aligned tags from each of the libraries from which the data come.
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