calcPrototype {HELP} | R Documentation

## Calculate prototype

### Description

Calculates prototype (trimmed mean) across all samples

### Usage

    calcPrototype(x, ...)

### Arguments

`x` | a numeric matrix, where each column represents a different sample
`...` | Arguments to be passed to methods (see `calcPrototype-methods`): `element` which element of `AssayData` to use for a given `ExpressionSet` input (default is "exprs") `samples` which samples to use as data. Can be a vector of characters matching sample names, integers indicating which samples to choose, or a mixture of the two. If NULL (default), all samples will be used. `center` logical; if TRUE (default) samples will be mean-centered before protototype calculation. If FALSE, this mean-centering step will be skipped `trim` the fraction (0 to 0.5, default is 0.1) of observations to be trimmed from each end of each row and column in `x` before the mean is computed. `verbose` logical; if TRUE (default) progress will be output to screen. If FALSE, no output will be displayed. `...` other arguments to be passed to `mean`. See `mean`.

### Value

Returns a vector of numerical data, representing the prototype ([trimmed] mean) of all samples in x.

### Author(s)

Mark Reimers (mreimers@vcu.edu), Reid F. Thompson (rthompso@aecom.yu.edu)

### See Also

`calcPrototype-methods`, `mean`

### Examples

    #demo(pipeline,package="HELP")

    x <- matrix(data=rep(1:1000,10),nrow=1000,ncol=10)
    x <- x*(sample(1:100/100,size=10000,replace=TRUE))
    x <- t(t(x)-1000*(1:10))
    x[c(1:10,991:1000),]
    x.avg <- calcPrototype(x)
    x.avg[c(1:10,991:1000)]

    #rm(x,x.avg)

[Package HELP version 1.0.0 Index]