HEMDAG (version 2.1.3)

Do.flat.scores.normalization: Flat scores normalization

Description

High level functions to normalize a flat scores matrix w.r.t. max normalization (MaxNorm) or quantile normalization (Qnorm)

Usage

Do.flat.scores.normalization(norm.type = "MaxNorm", flat.file = flat.file,
  flat.dir = flat.dir, flat.norm.dir = flat.norm.dir)

Arguments

norm.type

can be one of the following two values:

• MaxNorm (def.): each score is divided w.r.t. the max of each class;

• Qnorm: a quantile normalization is applied. Library preprocessCore is used.

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

Value

the matrix of the scores flat normalized w.r.t. MaxNorm or Qnorm in flat.norm.dir

Details

To apply the quantile normalization the preprocessCore library is uded.

Examples

# NOT RUN {
data(scores);
if(!dir.exists("data")){
	dir.create("data");
}
if(!dir.exists("results")){
	dir.create("results");
}
save(S,file="data/scores.rda");
flat.dir <- "data/";
flat.norm.dir <- "results/";
flat.file <- "scores";
norm.types <- c("MaxNorm","Qnorm");
for(norm.type in norm.types){
	Do.flat.scores.normalization(norm.type=norm.type, flat.file=flat.file, 
flat.dir=flat.dir, flat.norm.dir=flat.norm.dir);
}
# }