make.transformation {metaseqR} | R Documentation

## Calculates several transformation of counts

### Description

Returns a list of transformed (normalized) counts, based on the input count matrix data.matrix. The data transformations are passed from the `export.scale` parameter and the output list is named accordingly. This function is intended mostly for internal use but can also be used independently.

### Usage

        make.transformation(data.matrix, export.scale,
            scf = NULL, log.offset = 1)

### Arguments

`data.matrix` | the raw or normalized counts matrix. Each column represents one input sample.
`export.scale` | a character vector containing one of the supported data transformations (`"natural"`, `"log2"`, `"log10"`,`"vst"`). See also the main help page of metaseqr.
`scf` | a scaling factor for the reads of each gene, for example the sum of exon lengths or the gene length. Divided by each read count when `export.scale="rpgm"`. It provides an RPKM-like measure but not the actual RPKM as this normalization is not supported.
`log.offset` | a number to be added to each element of data.matrix in order to avoid Infinity on log type data transformations.

### Value

A named list whose names are the elements in export.scale. Each list member is the respective transformed data matrix.

### Author(s)

Panagiotis Moulos

### Examples

    data.matrix <- round(1000*matrix(runif(400),100,4))
    rownames(data.matrix) <- paste("gene_",1:100,sep="")
    colnames(data.matrix) <- c("C1","C2","T1","T2")
    tr <- make.transformation(data.matrix,c("log2","vst"))
    head(tr$vst)

[Package metaseqR version 1.28.0 Index]