transformAssay {MatrixQCvis} | R Documentation

## Transform the (count/intensity) values of a 'data.frame', 'tbl' or 'matrix'

### Description

The function 'transformAssay' transforms the (count/intensity) values of a 'matrix'. It uses either 'log2', variance stabilizing normalisation ('vsn') or no transformation method (pass-through, 'none'). The object 'x' has the samples in the columns and the features in the rows.

### Usage

    transformAssay(a, method = c("none", "log2", "vsn"))

### Arguments

`a` | 'matrix' with samples in columns and features in rows
`method` | 'character', one of '"none"', '"log2"' or '"vsn"'

### Details

Internal use in 'shinyQC'.

### Value

'matrix'

### Examples

    a <- matrix(1:1000, nrow = 100, ncol = 10,
            dimnames = list(1:100, paste("sample", 1:10)))
    transformAssay(a, "none")
    transformAssay(a, "log2")
    transformAssay(a, "vsn")

[Package MatrixQCvis version 1.0.0 Index]