r3Cseq-class: r3Cseq objects

In r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

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

r3Cseq documentation built on Nov. 8, 2020, 6:26 p.m.