PreprocessViews2-class: A container for storing views of preprocessed data

In cancer-genomics/trellis: Somatic structural variant analysis

A container for storing views of preprocessed data

Description

This class directly extends the BamViews class and provides views to intermediate data (saved to disk) from the analysis of one or more bam files.

Usage

PreprocessViews2(object)

## S4 replacement method for signature 'PreprocessViews2,ANY'
rowRanges(x) <- value

## S4 method for signature 'PreprocessViews2'
rowRanges(x, ...)

## S4 method for signature 'PreprocessViews2'
seqlevels(x)

## S4 method for signature 'PreprocessViews2'
seqinfo(x)

## S4 replacement method for signature 'PreprocessViews2'
seqinfo(x) <- value

Arguments

object	can be missing or an existing BamViews object
x	a PreprocessViews2 object
value	an object of class seqinfo
...	ignored

Value

A PreprocessViews2 object

Slots

scale

a length-one numeric vector. We scale numeric data by the value of scale, round to the nearest integer, and then save as an integer. This slot is for internal use only.

See Also

See paths for the character-vector of file paths to the intermediate data.

Examples

PreprocessViews2()
paths(PreprocessViews2())
pviews <- PreprocessViews2()
paths(pviews) <- character()
paths(pviews)

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.