r3Cseq-class {r3Cseq} | R Documentation

## 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

### Author(s)

S. Thongjuea

### See Also

r3CseqCommon, r3CseqInBatch

### Examples

    # See the vignette

[Package r3Cseq version 1.28.0 Index]