comp.FC {DEDS} | R Documentation |

## Computing Fold Change for Differential Expression

### Description

`comp.FC`

returns a function of one argument with bindings for
`L`

, `is.log`

and `FUN`

. This function accepts a
microarray data matrix as its single argment, when evaluated, computes
fold change for each row of the matrix.

### Usage

comp.FC(L = NULL, is.log = TRUE, FUN = mean)

### Arguments

`L` |
A vector of integers corresponding to observation (column)
class labels. For *k* classes, the labels must be integers
between 0 and *k-1*. |

`is.log` |
A logical variable indicating whether the data has been
logged. |

`FUN` |
The summary statistics function used to calcuate fold
change, the default is set as `mean` , the user can also
use `median` |

.

### Details

The function returned by `comp.FC`

calculates fold change for each row
of the matrix, given specific class labels. If `is.log=TRUE`

,
fold change is calculated by substraction; if `is.log=FALSE`

,
fold change is calculated by division.

### Value

`comp.FC`

returns a function with bindings for `L`

,
`is.log`

and `FUN`

, which calculates and returns a vector of
fold changes for each row in the data matrix.

### Author(s)

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,

Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

### See Also

`comp.t`

,`comp.F`

### Examples

X <- matrix(rnorm(1000,0,0.5), nc=10)
L <- rep(0:1,c(5,5))
# genes 1-10 are differentially expressed
X[1:10,6:10]<-X[1:10,6:10]+1
f <- comp.FC(L=L)
f.X <- f(X)

[Package

*DEDS* version 1.0.3

Index]