esApply {Biobase} | R Documentation

## Apply for the Expression Data in 'exprSet'

### Description

`esApply` is a wrapper to apply for use with `exprSet`s and `eSet`s. Because the application of a function to the rows of the expression array usually involves variables in the `phenoData` slot we have used a special evaluation paradigm here. The function `FUN` may reference any data in phenoData by name.

Consider defining the function as a method for 'exprSet', 'eSet'

### Usage

    esApply(X, MARGIN, FUN, ...)

### Arguments

`X` | An instance of class `exprSet`. It is assumed that `X` has information on gene expression for G genes in N tissue samples.
`MARGIN` | The margin to apply to, either 1 for rows or 2 for columns.
`FUN` | Any function
`...` | Additional parameters for `FUN`

### Details

The `phenoData` from `X` is installed in an environment. This environment is installed as the environment of `FUN`. This will then provide bindings for any symbols in `FUN` that are the same as the names of the `phenoData` of `X`. If `FUN` has an environment already it is retained but placed after the newly created environment. Some variable shadowing could occur under these circumstances.

### Value

The result of `apply(exprs(X),MARGIN, FUN, ...)`.

### Author(s)

V.J. Carey <stvjc@channing.harvard.edu>, R. Gentleman

### See Also

`apply`, `exprSet`

### Examples

    data(sample.exprSet.1)

    # we know that eset has covariates in the pData called "cov1" and "cov2"
    # here cov1 is an unbound value, it will be resolved by using the pData
    # here are two functions conforming to the esApply protocol

    mytt.demo <- function(y) {
     ys <- split( y, cov1 )
     t.test( ys[[1]], ys[[2]] )$p.value
     }

    # obtain the p value of the slope associated with cov2, adjusting for cov1
    # (if we were concerned with sign we could save the z statistic instead at coef[3,3]
    myreg.demo <- function( y ) {
       summary(lm(y~cov1+cov2))$coef[3,4]
    }

    newt <- esApply( sample.exprSet.1, 1, mytt.demo )

    # a resampling method
    resamp <- function( ESET ) {
     ntiss <- ncol(exprs(ESET))
     newind <- sample(1:ntiss, size=ntiss, replace=TRUE)
     ESET[newind,]
     }

    # a filter
    q3g100filt <- function( eset ) {
     apply( exprs(eset), 1, function(x)quantile(x,.75)>100 )
     }

    # filter after resampling and then apply
    set.seed(123)
    rest <- esApply( { bool <- q3g100filt(resamp(sample.exprSet.1)); sample.exprSet.1[bool,] }, 1,
    mytt.demo )

[Package Biobase version 1.12.2 Index]