| utilities {EBarrays} | R Documentation |
Utilitiy functions for the EBarrays package
createExprSet(datafile, repfile) ebPatterns(x)
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.
|
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.
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.
Christina Kendziorski, Michael Newton and Deepayan Sarkar
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)