Class to contain result of a vsn fit

Description

Class to contain result of a vsn fit

Creating Objects

new("vsn") vsn2(x) with x being an ExpressionSet.

Slots

coefficients:

A 3D array of size (number of strata) x (number of columns of the data matrix) x 2. It contains the fitted normalization parameters (see vignette).

strata:

A factor of length 0 or n. If its length is n, then its levels correspond to different normalization strata (see vignette).

mu:

A numeric vector of length n with the fitted parameters hat{μ}_k, for k=1,...,n.

sigsq:

A numeric scalar, hat{σ}^2.

hx:

A numeric matrix with 0 or n rows. If the number of rows is n, then hx contains the transformed data matrix.

lbfgsb:

An integer scalar containing the return code from the L-BFGS-B optimizer.

hoffset:

Numeric scalar, the overall offset c- see manual page of vsn2.

calib:

Character of length 1, see manual page of vsn2.

Methods

[

Subset

dim

Get dimensions of data matrix.

nrow

Get number of rows of data matrix.

ncol

Get number of columns of data matrix.

show

Print a summary of the object

exprs

Accessor to slot hx.

coef, coefficients

Accessors to slot coefficients.

Author(s)

Wolfgang Huber

See Also

vsn2

Examples

  data("kidney")
  v = vsn2(kidney)
  show(v)
  dim(v)
  v[1:10, ]

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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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(vsn)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/vsn/class.vsn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: vsn
> ### Title: Class to contain result of a vsn fit
> ### Aliases: class:vsn vsn-class [,vsn-method dim,vsn-method
> ###   nrow,vsn-method ncol,vsn-method show,vsn-method exprs,vsn-method
> ###   coef,vsn-method coefficients,vsn-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>   data("kidney")
>   v = vsn2(kidney)
>   show(v)
vsn object for n=8704 features and d=2 samples.
sigsq=0.005
hx: 8704 x 2 matrix.
>   dim(v)
[1] 8704    2
>   v[1:10, ]
vsn object for n=10 features and d=2 samples.
sigsq=0.005
hx: 10 x 2 matrix.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>