SRSet-class: (Legacy) A base class for Roche experiment-wide data
In ShortRead: FASTQ input and manipulation

Description Objects from the Class Slots Extends Methods Author(s) Examples

This class coordinates phenotype (sample) and sequence data, primarily as used on the Roche platform.

Conceptually, this class has reads from a single experiment represented as a long vector, ordered by sample. The readCount slot indicates the number of reads in each sample, so that the sum of readCount is the total number of reads in the experiment. The readIndex field is a light-weight indicator of which reads from all those available that are currently referenced by the SRSet.

Objects of this class are not usually created directly, but instead are created by a derived class, e.g., RocheSet.

sourcePath:: Object of class "ExperimentPath", containing the directory path where sequence files can be found.
readIndex:: Object of class "integer" indicating specific sequences included in the experiment.
readCount:: Object of class "integer" containing the number of reads in each sample included in the experiment. The sum of this vector is the total number of reads.
phenoData:: Object of class "AnnotatedDataFrame" describing each sample in the experiment. The number of rows of phenoData equals the number of elements in readCount.
readData:: Object of class "AnnotatedDataFrame" containing annotations on all reads.

Class ".ShortReadBase", directly.

experimentPath: signature(object = "SRSet"): return the ExperimentPath associated with this object.
phenoData: signature(object = "SRSet"): return the phenoData associated with this object.
readCount: signature(object="SRSet"):
readIndex: signature(object="SRSet"):
readData: signature(object="SRSet"):
sourcePath: signature(object="SRSet"): Retrieve the corresponding slot from object.
show: signature(object = "SRSet"): display the contents of this object.
detail: signature(x = "SRSet"): provide more extensive information on the object.