PatCNVSession-class: Class '"PatCNVSession"'

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

This class of objects is returned by the createSession function to represent a session of patternCNV project, specifically, exon information, sample information and sample WIG files.

Objects from the Class

Objects can be created by calls of the form new("PatCNVSession", ...).

Slots

exon.info:

Object of class "GRanges": the corresponding genomic ranges for the observed exons

sample.info:

Object of class "data.frame": sample information, containing "sample.name", "sample.type", etc.

output.DIR:

Object of class "list": output directory information

pattern.file:

Object of class "list": average- and variability filenames

Misc:

Object of class "list": other information

N.exon:

Object of class "numeric": number of exons

N.sample:

Object of class "numeric": number of samples

Methods

exonInfo

signature(obj = "PatCNVSession"): retrieve exon information

exonNum

signature(obj = "PatCNVSession"): number of exons

sampleInfo

signature(obj = "PatCNVSession"): retrieve sample information

sampleNum

signature(obj = "PatCNVSession"): number of samples

show

signature(object = "PatCNVSession"): summarize patternCNV session information

summary

signature(object = "PatCNVSession"): summarize patternCNV session information

Author(s)

Chen Wang

See Also

PatCNVData-class

Examples

#=== load a simulation example
config.filename <- "sim1.ini"
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== test if session is created
summary(sim.session)

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.