r3CseqInBatch-class: r3CseqInBatch objects
Description
The r3CseqInBatch class is the extended class from r3CseqCommon class. It is a general container for storing
and manipulating a set of input parameters, RangeData of interactions regions from r3Cseq analysis for replicates data sets.
Extends
Class r3CseqCommon, directly.Slots
organismName- Object of class
"character" the version of
particular assembly genome from UCSC (e.g. mm9, hg18, hg19) . The package supports
three genome assemblies consisting of mouse (mm9), and human (hg18, hg19). restrictionEnzyme- Object of class
"character" this is the primary
restriction enzyme name using in 3C-Seq experiment viewpoint_chromosome- Object of class
"character"
chromosome name of where is the viewpoint located eg. chr10, chrX etc.
viewpoint_primer_forward- Object of class
"character"
the forward primer DNA sequences for the viewpoint amplification viewpoint_primer_reverse- Object of class
"character"
the reverse primer DNA sequences for the viewpoint amplification expReadCount- Object of class
"RangedData"
the read count in experiment contrReadCount- Object of class
"RangedData"
the read count in control expRPM- Object of class
"RangedData"
the normalized read read per million in experiment contrRPM- Object of class
"RangedData"
the normalized read read per million in control expInteractionRegions- Object of class
"RangedData"
the identified interaction regions in experiment contrInteractionRegions- Object of class
"RangedData"
the identified interaction regions in control isControlInvolved- Object of class
"logical"
the logical to ask whether the control is involved in the analysis or not bamFilesDirectory- Object of class
"character"
the path name of directory that contains BAM files BamExpFiles- Object of class
"vector"
the file names of BAM files in the experiment BamContrFiles- Object of class
"vector"
the file names of BAM files in the control expBatchLabel- Object of class
"vector"
the labeled experiment names contrBatchLabel- Object of class
"vector"
the labeled control names readCountTable- Object of class
"RangedData"
the read count table RPMsTable- Object of class
"RangedData"
the normalized read per million table expBatchLibrarySize- Object of class
"vector"
the library size of each experiment contrBatchLibrarySize- Object of class
"vector"
the library size of each control expBatchReadLength- Object of class
"vector"
the read length of experiments contrBatchReadLength- Object of class
"vector"
the read length of controls