cofVar {coexnet} | R Documentation

## Calculating the coefficient of variation for expression matrix.

### Description

This function calculates the mean and the coefficient of variation to each row (genes or probesets) in an expression matrix in two ways: i) in the whole matrix ii) for the specific phenotype (case or control).

### Usage

    cofVar(expData, complete = TRUE, treatment = NULL, type = NULL)

### Arguments

`expData` | The whole normalized expression matrix, rows: genes or probeset, columns: samples, it may be stored in a SummarizedExperiment object.
`complete` | Boolean to define if the function uses the whole expression matrix, by default TRUE.
`treatment` | A numeric vector with 0s and 1s for each sample in the expression matrix, the 0 expresses the control samples and 1 expresses the case samples, by default is NULL.
`type` | It can be "case" to calculate the mean and the coefficient of variation for the case samples or, otherwise, "control" to obtain these two values for the control samples.

### Value

The expression matrix with two new columns, the first one with the averages and the other one with the coefficient of variation values.

### Author(s)

Juan David Henao <judhenaosa@unal.edu.co>

### Examples

    ## Creating the expression matrix

    # The matrix have 200 genes and 20 samples

    n <- 200
    m <- 20

    # The vector with treatment and control samples

    treat <- c(rep(0,10),rep(1,10))

    # Calculating the expression values normalized

    mat <- as.matrix(rexp(n, rate = 1))
    norm <- t(apply(mat, 1, function(nm) rnorm(m, mean=nm, sd=1)))

    ## Calculating the mean and the coefficient of variation

    # For the whole expression matrix

    complete <- cofVar(norm)
    head(complete)

    # For the case samples

    case <- cofVar(expData = norm,complete = FALSE,treatment = treat,type = "case")
    head(case)

[Package coexnet version 1.2.0 Index]