Description Usage Arguments Details Author(s) References Examples
This function has been deprecated. You could better use gsea
instead.
This function performs the second step in the process of obtaining a
GSEAlike plot.
It computes the NES (normalized enrichment score), p values and fdr
(false discovery rate) for all variables and signatures. A
gseaSignaturesSign
or gseaSignaturesVar
object will
be needed as input (these objects can be obtained with the
gseaSignatures
function).
For an overview of the output use the summary
method.
The next step after using the gseaSignificance
function would be using
the plot
method.
1  gseaSignificance(x,p.adjust.method='none',pval.comp.method='original',pval.smooth.tail=TRUE)

x 

p.adjust.method 
p adjustment method to be used. Common options
are 'BH', 'BY', 'bonferroni' or 'none'. All available options and
their explanations can be found on the 
pval.comp.method 
the p value computation method. Has to be one of 'signed' or 'original'. The default one is 'original'. See details for more information. 
pval.smooth.tail 
if we want to estimate the tail of the ditribution where the pvalues will be generated. 
The simulated enrichment scores and the calculated one are used to find the p value.
P value calculation depends on the parameter
pval.comp.method
. The default value is 'original'. In 'original'
we are simply computing the proportion of anbolute simulated ES which
are larger than the observed absolute ES. In 'signed' we are computing
the proportion of simulated ES which are larger than the observed ES (in
case of having positive enrichment score) and the proportion of
simulated ES which are smaller than the observed ES (in case of having
negative enrichment score).
Evarist Planet
Aravind Subramanian, (October 25, 2005) Gene Set Enrichment Analysis. www.pnas.org/cgi/doi/10.1073/pnas.0506580102
C.A. Tsai and J.J. Chen. Kernel estimation for adjusted pvalues in multiple testing. Computational Statistics & Data Analysis http://econpapers.repec.org/article/eeecsdana/v_3a51_3ay_3a2007_3ai_3a8_3ap_3a38853897.htm
1  #for examples see the help file of gseaSigntaures: ?gseaSignatures

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