r3Cseq-class: r3Cseq objects
Description
The r3Cseq 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
, and the raw reads GRanged data of the genome-wide interaction signal generated by next-generation sequencing.
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 alignedReadsBamExpFile- Object of class
"character"
the file name of experiment in BAM format alignedReadsBamContrFile- Object of class
"character"
the file name of control in BAM format expLabel- Object of class
"character"
the experiment name contrLabel- Object of class
"character"
the control name expLibrarySize - Object of class
"integer"
the library size of experiment contrLibrarySize - Object of class
"integer"
the library size of control expReadLength- Object of class
"integer"
the read length of experiment contrReadLength- Object of class
"integer"
the read length of experiment expRawData- Object of class
"GRanges"
the raw reads found in experiment contrRawData- Object of class
"GRanges"
the raw reads found in control