getdata: Check dataset

In SamGG/made4: Multivariate analysis of microarray data using ADE4

Description

This function is called by array2ade4 which converts input data into a data.frame suitable for analysis in ADE4. This function is not normally called by the user

Usage

getdata(arraydata)

Arguments

arraydata

A matrix, data.frame, ExpressionSet or marrayRaw-class or RangedSummarizedExperiment, SummarizedExperiment. If the input is gene expression data in a matrix or data.frame. The rows and columns are expected to contain the variables (genes) and cases (array samples) respectively.

Details

bga and other functions in made4 call this function and it is generally not necessary to call this directly. array2ade4 calls getdata, and will accept a matrix,data.frame, ExpressionSet or marrayRaw-class, SummarizedExperiment,RangedSummarizedExperiment format. It will also transpose data or add a integer to generate a positive data matrix. If the input data contains NA, these must first be removed or imputed (see the R libraries impute() or pamr()).

Value

Returns a data.frame suitable for analysis by ade4 or made4 functions.

Note

This is not normally called by a user. Internal function.

Author(s)

Aedin Culhane

See Also

array2ade4

SamGG/made4 documentation built on Sept. 29, 2020, 1:33 p.m.