utilities {EBarrays}R Documentation

Utility functions for the EBarrays package

Description

Utilitiy functions for the EBarrays package

Usage

createExprSet(datafile, repfile)
ebPatterns(x)

Arguments

datafile file with data
repfile file with replication information
x x can be a character vector (of length > 2) (see example), or an arbitrary connection which should provide patterns, one line for each pattern. If x is a character vector of length 1, it is assumed to be the name of a file (since there's no point in a patterns object with only one pattern) which is then opened and treated as a connection.

Details

ebPatterns creates objects that represent a collection of hypotheses to be used by emfit.

It, along with createExprSet, also provides back compatibility with an earlier version of EBarrays, which required input data to be in a very specific format. For example, the (earlier) usage cleanup(NULL, "data.txt", "repfile.txt", "patternfile.txt") can be replaced by createExprSet("data.txt", "repfile.txt") and ebPatterns("patternfile.txt").

Unless one has data in this particular format, the createExprSet function can be safely ignored.

Value

createExprSet creates an object of class "exprSet".
ebPatterns creates an Object of class ``ebarraysPatterns'', to be used in other functions such as emfit. This is nothing more than a list (and can be treated as such as far as indexing goes) and is used only for method dispatch.

Author(s)

Christina Kendziorski, Michael Newton and Deepayan Sarkar

See Also

emfit

Examples

patterns <- ebPatterns(c("1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1",
                         "1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2"))
show(patterns)

[Package EBarrays version 1.8.1 Index]