PatCNVData-class: Class '"PatCNVData"'

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

Description

This class of objects can be returned by the scanMultiCovg or computeMultiCNV functions to represent patternCNV results, specifically, coverage, CNV log2-ratio and FDR results.

Objects from the Class

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

Slots

eSet:

Object of class SummarizedExperiment: a set container where rows represent exons and columns represent samples

method.info:

Object of class "list": a list of method information

datatype.vec:

Object of class "character": character vector of different data types

sample.covg.vec:

Object of class "numeric": numerical vector of sample-level coverage

N.exon:

Object of class "numeric": number of exons

N.sample:

Object of class "numeric": number of samples

Methods

avgExonCoverage

signature(obj = "PatCNVData"): compute average coverage of exons across samples

cnvMatrix

signature(obj = "PatCNVData"): retrieve log2ratio CNV matrix

coverageMatrix

signature(obj = "PatCNVData"): retrieve coverage matrix

exonInfo

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

exonNum

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

fdrMatrix

signature(obj = "PatCNVData"): retrieve FDR matrix

sampleCoverage

signature(obj = "PatCNVData"): summarize sample-level coverage

sampleInfo

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

sampleNum

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

show

signature(object = "PatCNVData"): summarize patternCNV data information

summary

signature(object = "PatCNVData"): summarize patternCNV data information

Author(s)

Chen Wang

See Also

PatCNVSession-class

Examples

#=== load simulated data with pre-computed coverage and CNV
data(sim.cnvData)
 
#=== display class of simulated data
typeof(sim.cnvData)

#=== print basic information of the created object
summary(sim.cnvData)

#=== list coverage information of a few top exons of sample "n3" and "n5"
head(coverageMatrix(sim.cnvData, c("n3","n5")))

#=== display CNV log2ratio of exons of gene "SLC25A17" of samples "n2" and "n5"
cnvMatrix(sim.cnvData, c("n2","n5"),"SLC25A17")

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