Class "alignmentClass"

Description

The alignmentClass class records information about a set of alignments of high-throughput sequencing data to a genome.

Slots

alignments:

Object of class "GRanges". Stores information about the alignments. See Details.

libnames:

Object of class "character". The names of the libraries for which alignment data exists.

replicates:

Object of class "factor". Replicate information for each of the libraries. See Details.

Details

The alignments slot is a GRanges object defining the location of aligned objects to a reference genome.

The replicates slot is a vector of factors such that the ith sample is a replicate of the jth sample if and only if @replicates[i] == @replicates[j].

The libnames slot is a vector defining the names of the libraries described by the object.

Methods

[

signature(x = "alignmentClass"): ...

dim

signature(x = "alignmentClass"): ...

initialize

signature(.Object = "alignmentClass"): ...

show

signature(object = "alignmentClass"): ...

Author(s)

Thomas J. Hardcastle

See Also

alignmentData alignmentMeth

Results