Usage
runGSA(nData, labels, gmtfile, chip = "hgu133plus2", np = 1000,
minsize = 10, maxsize = 800, resp.type = "Two class unpaired",
fdr = 0.25)
Arguments
nData
a matrix or a data frame of expression data.
Each row of 'data' must correspond to a gene, and each column to a
sample.
labels
a vector of length 'ncol(data)' containing the class labels
of the samples.
In "Two class unpaired", 'labels' should be a vector containing 0's
(specifying the samples of, e.g., the control group) and 1's
(specifying, e.g., the case group)
gmtfile
a character string corresponding to the path file of a
gmt file, corresponding to a gene set collection (a list).
chip
a character string corresponding to the chip type of the
data.
np
a numerical value corresponding to the number of
permutations.
minsize
a numerical value corresponding to the minimum number
of genes in genesets to be considered.
maxsize
a numerical value corresponding to the minimum number
of genes in genesets to be considered.
resp.type
Problem type: "quantitative" for a continuous parameter;
"Two class unpaired" ; "Survival" for censored survival
outcome; "Multiclass" : more than 2 groups.
"Two class paired" for paired outcomes.
fdr
a numerical value corresponding to the fdr threshold.