cghRA.series-class: Class '"cghRA.series"'

In cghRA: Array CGH Data Analysis and Visualization

Description

Objects from this class are collections of cghRA.regions objects, and provide various methods for CGH series analysis.

Objects from this class should always be produced by the cghRA.series constructor.

Extends

All reference classes extend and inherit methods from envRefClass.

Fields

arrays:

A possibly named list of cghRA.regions objects.

name:

Single character value, the custom name of the series.

Methods

add(object):

Add an object to the series

applyMethod(.method, ..., .simplify = , .quiet = ):

Calls a method on each array of the series
- .method : single character value, the method to be called.
- ... : arguments to be passed to the method.
- .simplify : same behavior as sapply() 'simplify' argument.
- .quiet : single logical value, whether to print iterations or not.

check(warn = ):

Raises an error if the object is not valid, else returns TRUE

get(arrayName):

Returns an element from the series

getArrayNames():

Returns a vector of array names

initialize(name = , arrays = , ...):

last():

Refers to the last array added in the series

LRA(value = , tracks = , ...):

Apply the LRA() function to list Long Recurrent Abnormalities (Lenz et al, PNAS 2008).
- value : single character value, the name of the column to use as copy number estimate ('copies' or 'logRatio').
- tracks : single logical value, whether to convert output to track.table class or not.

parallelize(value = , quiet = , tracks = , ...):

Apply the parallelize() function to build a summary matrix of the series.
- tracks : single logical value, whether to convert output to track.table class or not.

penetrance(tracks = , ...):

Apply the penetrance() function to compute the proportion of altered samples for each genomic position.
- tracks : single logical value, whether to convert output to track.table class or not.

pool(tracks = , value = , group = , states = , others = , quiet = ):

Collect and pool all alterated segments from the various samples of the series.
- tracks : single logical value, whether to convert output to track.table class or not.
- value : column on which apply a filtering.
- group : single logical value, whether to visually group segments per samples or not (valid only for tracks=TRUE).
- states : list of states, see penetrance help page for details. If 'states' is not empty, segments without state will be filtered out.
- others : character vector, names of other columns to keep.
- quiet : single logical value, whether to throw diagnosis messages or not.

SRA(value = , tracks = , ...):

Apply the SRA() function to list Short Recurrent Abnormalities (Lenz et al, PNAS 2008).
- value : single character value, the name of the column to use as copy number estimate ('copies' or 'logRatio').
- tracks : single logical value, whether to convert output to track.table class or not.

STEPS(tracks = , ...):

Apply the STEPS() function to prioritize commonly altered regions.
- tracks : single logical value, whether to convert output to track.table class or not.

The following methods are inherited (from the corresponding class):

• callSuper (envRefClass)

• copy (envRefClass)

• export (envRefClass)

• field (envRefClass)

• getClass (envRefClass)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• show (envRefClass, overloaded)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

cghRA.series, cghRA.regions

cghRA documentation built on May 2, 2019, 3:34 a.m.