vsnInput {vsn} | R Documentation

## Class to contain input data and parameters for vsn functions

### Description

Class to contain input data and parameters for vsn functions

### Creating Objects

`new("vsnInput")`

### Slots

`x`:

  A numeric matrix with the input data.

`reference`:

  An object of `vsn`, typically this would have been obtained from a previous fit to a set of reference arrays (data).

`strata`:

  A factor of length 0 or n. If its length is n, then its levels correspond to different normalization strata (see `vsn2`).

`ordered`:

  Logical scalar; are the rows reordered so that the strata are contiguous.

`lts.quantile`:

  Numeric scalar, see`vsn2`.

`subsample`:

  Integer scalar, see`vsn2`.

`verbose`:

  Logical scalar, see`vsn2`.

`calib`

  Character of length 1, see manual page of `vsn2`.

`pstart`:

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

`optimpar`:

  List with parameters for the numerical optimiser `L-BFGS-B`; see the 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

### Author(s)

Wolfgang Huber

### See Also

`vsn2`

[Package vsn version 3.58.0 Index]