foldchange {gtools}

Compute fold-change or convert between log-ratio and fold-change.

Description

foldchange computes the fold change for two sets of values. logratio2foldchange converts values from log-ratios to fold changes. foldchange2logratio does the reverse.

Usage

foldchange(num, denom)

logratio2foldchange(logratio, base = 2)

foldchange2logratio(foldchange, base = 2)

Arguments

num, denom

vector/matrix of numeric values

logratio

vector/matrix of log-ratio values

base

Exponential base for the log-ratio.

foldchange

vector/matrix of fold-change values

Details

Fold changes are commonly used in the biological sciences as a mechanism for comparing the relative size of two measurements. They are computed as: \frac{num}{denom} if num>denom, and as \frac{-denom}{num} otherwise.

Fold-changes have the advantage of ease of interpretation and symmetry about num=denom, but suffer from a discontinuity between -1 and 1, which can cause significant problems when performing data analysis. Consequently statisticians prefer to use log-ratios.

Value

A vector or matrix of the same dimensions as the input containing the converted values.

Functions

• foldchange(): Compute fold-change.

• logratio2foldchange(): Compute foldchange from log-ratio values.

• foldchange2logratio(): Compute log-ratio from fold-change values.

Author(s)

Gregory R. Warnes [e-mail]

Examples

a <- 1:21
b <- 21:1

f <- foldchange(a, b)

cbind(a, b, f)