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 1.2.0 Index]