copynumber: Retrieve copynumber data from cgh objects.

In CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

Description

These generic functions access the copynumber values of assay data stored in an object derived from the cghRaw-class, cghSeg-class or cghCall-class.

Usage

copynumber(object)
copynumber(object) <- value
segmented(object)
segmented(object) <- value
calls(object)
calls(object) <- value

Arguments

object	Object derived from class cghRaw, cghSeg, or cghCall
value	Matrix with rows representing features and columns samples.

Value

copynumber returns a matrix of copynumber values;

Author(s)

Sjoerd Vosse

See Also

cghRaw-class, cghSeg-class, cghCall-class

Examples

	data(WiltingCalled)
	log2ratios <- copynumber(WiltingCalled)
	segments <- segmented(WiltingCalled)
	calls <- calls(WiltingCalled)	

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: marray
Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

CGHbase documentation built on Nov. 8, 2020, 5:04 p.m.