concomp-class: Connected Component

In pkimes/spliceclust: Visualization and Clustering of Spliced Components

Description

S4 class encapsulating exon and junction information for a single "connected component" object.

Usage

concomp(obj, ...)

## S4 method for signature 'GRangesList'
concomp(obj)

## S4 method for signature 'data.frame'
concomp(obj)

## S4 method for signature 'concomp'
eRanges(object)

## S4 method for signature 'concomp'
jRanges(object)

## S4 method for signature 'concomp'
eCoverage(object)

## S4 method for signature 'concomp'
jCoverage(object)

## S4 replacement method for signature 'concomp'
eRanges(object) <- value

## S4 replacement method for signature 'concomp'
jRanges(object) <- value

## S4 replacement method for signature 'concomp'
eCoverage(object) <- value

## S4 replacement method for signature 'concomp'
jCoverage(object) <- value

## S4 method for signature 'concomp'
show(object)

Arguments

obj	primary input to concomp constructor (see Details for more information on supported signatures)
...	other parameters to be passed to constructor
object	a concomp object for slot setters and getters, and show method
value	new value for concomp slot

Details

The constructor method obj parameter can be either:

• a GRangesList with two GRanges named "e" and "j" corresponding to exon and junction ranges and coverage for a collection of samples to be used to construct a concomp object. Both GRanges must have one metadata for each sample (named sequentially: 's1', 's2', ...), giving the corresponding exon or splice junction coverages.

• a data.frame with gene model columns: 'chr', 'seqlengths', 'gStart', 'gStop', and 'kind' (e.g. 'e' or 'j'), as well as per-sample coverage columns: 's1', 's2', ...

Methods (by generic)

• eRanges: get eRanges slot

• jRanges: get jRanges slot

• eCoverage: get eCoverage slot

• jCoverage: get jCoverage slot

• eRanges<-: set eRanges slot

• jRanges<-: set jRanges slot

• eCoverage<-: set eCoverage slot

• jCoverage<-: set jCoverage slot

Slots

eRanges

a GRanges object containing the exonic information

jRanges

a GRanges object containing the junction information

eCoverage

a matrix of exon coverage values, e.g. RPKM, with number of rows equal to the length of exons, or NULL if not available

jCoverage

a matrix of junction coverage values, e.g. number of spanning reads, with number of rows equal to the length of juncs, or NULL if not available

Author(s)

Patrick Kimes

pkimes/spliceclust documentation built on Jan. 2, 2020, 4:44 a.m.