Class "denovoGeneExpr"

Description

denovoGeneExpr stores inferred expression for de novo splicing variants for a single gene. denovoGenomeExpr stores the information for several genes (typically, the whole genome).

Objects from the Class

Objects are returned by calcDenovo. When running calcDenovo on multiple genes results are returned in a denovoGenomeExpr object. Results for a single gene can be retrieved using the [[ operator as usual, which returns a denovoGeneExpr object.

Slots

posprob

data.frame containing the posterior probability of each model

expression

data.frame with the estimated expression of each variant under each model

variants

matrix indicating the exons contained in each variant.

integralSum

Sum of the log(integrated likelihood) + log(model prior probability) across all considered models.

npathDeleted

Number of paths that had 0 probability under all considered variants and had to be excluded for model fitting purposes.

priorq

Input parameter to calcDenovo

txLength

Length of transcripts in bp (including new isoforms found by casper)

Methods

show

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

names

Show names (island ids)

"["

Selects a subset of genes

"[["

Selects a single gene

posprob

Accesses the posterior probabilities of each model (slot posprob)

variants

Accesses the variant names and their respective exons

variants<-

Replaces the value of the slot variants (can be useful for renaming variants, for instance)

Author(s)

David Rossell

See Also

calcDenovo to create objects from the class. denovoExpr to obtain expression estimates from denovoGenomeExpr objects.

Examples

showClass("denovoGeneExpr")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/denovoGenomeExpr-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: denovoGeneExpr-class
> ### Title: Class "denovoGeneExpr"
> ### Aliases: denovoGeneExpr-class show,denovoGeneExpr-method
> ###   [,denovoGeneExpr,ANY,ANY,ANY-method [[,denovoGeneExpr,ANY,ANY-method
> ###   [[,denovoGeneExpr,ANY,ANY,ANY-method
> ###   [[,denovoGenomeExpr,ANY,ANY-method posprob variants variants<-
> ###   posprob,denovoGeneExpr-method variants,denovoGeneExpr-method
> ###   variants<-,denovoGeneExpr-method variants,denovoGenomeExpr-method
> ###   names,denovoGenomeExpr-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("denovoGeneExpr")
Class "denovoGeneExpr" [package "casper"]

Slots:
                                                                       
Name:       posprob   expression     variants  integralSum npathDeleted
Class:   data.frame   data.frame       matrix      numeric      numeric
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>