r3CseqInBatch-class {r3Cseq} | R Documentation

## 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

### Author(s)

S. Thongjuea

### See Also

r3CseqCommon, r3CseqInBatch

### Examples

    # See the vignette

[Package r3Cseq version 1.33.0 Index]