r3CseqInBatch-class: r3CseqInBatch objects

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

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

supatt-lab/r3Cseq documentation built on May 6, 2019, 4:34 p.m.