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Applies Variance Stabilising Transformation (DESeq2) to matrix

Source: R/transformation.R
transform_vst.Rd

Applies the Variance Stabilising Transformation (VST) performed by the DESeq2 package via the varianceStabilizingTransformation function. Includes a size factor normalisation prior to the VST. Only applies to a matrix of count.

Usage

transform_vst(mat, return_matrix_only = FALSE)

Arguments

mat

Numeric matrix, must contain integers only.

return_matrix_only

Logical, should only the transformed matrix be returned? If TRUE, the function will return a matrix. If FALSE, the function instead returns a list with the transformed data and potentially other information relevant to the transformation. Default value is FALSE.

Value

Depending on the return_matrix_only, either a matrix of transformed data, or a list with the following elements:

  • transformed_data: matrix of the transformed data;

  • info_transformation: A DESeqTransform object, with details about the transformation.