Description Usage Arguments Details Value Examples
High level functions to normalize a flat scores matrix w.r.t. max normalization (MaxNorm) or quantile normalization (Qnorm).
1 2 3 | Do.flat.scores.normalization(norm.type = "MaxNorm",
flat.file = flat.file, flat.dir = flat.dir,
flat.norm.dir = flat.norm.dir)
|
norm.type |
can be one of the following two values:
|
flat.file |
name of the flat scores matrix (without rda extension). |
flat.dir |
relative path to folder where flat scores matrix is stored . |
flat.norm.dir |
the directory where the normalized flat scores matrix must be stored. |
To apply the quantile normalization the preprocessCore package must be installed.
the matrix of the scores flat normalized w.r.t. MaxNorm or Qnorm in flat.norm.dir
.
1 2 3 4 5 6 7 8 9 | data(scores);
tmpdir <- paste0(tempdir(),"/");
save(S, file=paste0(tmpdir,"scores.rda"));
flat.dir <- flat.norm.dir <- tmpdir;
norm.types <- c("MaxNorm","Qnorm");
for(norm.type in norm.types){
Do.flat.scores.normalization(norm.type=norm.type, flat.file="scores",
flat.dir=flat.dir, flat.norm.dir=flat.norm.dir);
}
|
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