make.fold.change {metaseqR} | R Documentation

## Calculates fold changes

### Description

Returns a matrix of fold changes based on the requested contrast, the list of all samples and the data matrix which is produced by the metaseqr workflow. For details on the `contrast`, `sample.list` and `log.offset` parameters, see the main usage page of metaseqr. This function is intended mostly for internal use but can also be used independently.

### Usage

        make.fold.change(contrast, sample.list, data.matrix,
            log.offset = 1)

### Arguments

`contrast` | the vector of requested statistical comparison contrasts.
`sample.list` | the list containing condition names and the samples under each condition.
`data.matrix` | a matrix of gene expression data whose column names are the same as the sample names included in the sample list.
`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 matrix of fold change ratios, treatment to control, as these are parsed from contrast.

### 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")
    fc <- make.fold.change("Control_vs_Treatment",list(Control=c("C1","C2"),
        Treatment=c("T1","T2")),data.matrix)

[Package metaseqR version 1.27.13 Index]