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)