Class "annotatedGenome"

Description

The annotatedGenome class stores info about transcripts, usually created with procGenome from TxDb objects or user-provided .gtf files.

Objects from the Class

Objects are typically created with a call to procGenome (for known genomes) or to createDenovoGenome (for de novo genomes).

Slots

islands

GRangesList object with elements corresponding to gene islands. It indicates the start/end/name of each exon contained in the island

transcripts

Each element in the list corresponds to a gene island. It indicates the exons contained in each known variant.

exon2island

data.frame indicating the chromosome, start and end of each exon, and its corresponding gene island.

exonsNI

GRanges indicating the chromosome, start/end and id of each exon

aliases

data.frame indicating the aliases for each known transcript, i.e. transcripts having the exact same sequence of exons.

genomeVersion

Character indicating the genome version from which the object was build, e.g. "hg19"

dateCreated

Character indicating the date when the object was created. UCSC genomes chance from time to time, so that an "hg19" genome from Jan 2012 may not be exactly the same as in Dec 2012.

denovo

Logical variable. FALSE indicates that the object was created using available annotation only. TRUE indicates that new exons/islands were added based on the data observed in a particular RNA-seq experiment.

txLength

Numeric vector storing transcript lengths.

knownVars

List where each element corresponds to an island, and contains a character vector with names of isoforms that should be considered as known (i.e. always included in the model)

Methods

show

signature(object = "annotatedGenome"): Displays general information about the object.

Author(s)

Camille Stephan-Otto Attolini

See Also

procGenome and createDenovoGenome to create annotatedGenome objects.

Examples

showClass("annotatedGenome")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(casper)
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, xtabs

The following objects are masked from 'package:base':

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

Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/annotatedGenome-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotatedGenome-class
> ### Title: Class "annotatedGenome"
> ### Aliases: annotatedGenome annotatedGenome-class
> ###   show,annotatedGenome-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("annotatedGenome")
Class "annotatedGenome" [package "casper"]

Slots:
                                                                            
Name:        islands   transcripts     knownVars   exon2island       exonsNI
Class:   GRangesList          list          list    data.frame       GRanges
                                                                            
Name:        aliases genomeVersion   dateCreated      txLength        denovo
Class:    data.frame     character          Date       numeric       logical
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>