transformAssay: Transform the (count/intensity) values of a 'data.frame',...

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

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 log, log2, log10, 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", "log", "log2", "log10", "vsn"),
  .offset = 1
)

Arguments

a	matrix with samples in columns and features in rows
method	character, one of "none", "log", "log2", "log10", or "vsn"
.offset	numeric(1), offset to add when method set to "log", "log2", or "log10" and a contains values of 0, default to 1

Details

Internal use in shinyQC.

Value

matrix

Examples

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

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.