calcPrototype: Calculate prototype
In HELP: Tools for HELP data analysis

Description Usage Arguments Value Author(s) See Also Examples

Calculates prototype (trimmed mean) across all samples

1	calcPrototype(x, ...)

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.
\dots: other arguments to be passed to mean. See mean.

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

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

calcPrototype-methods, mean

#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)