Description Usage Arguments Value References Examples
View source: R/connectivityScore.R
A function for finding the connectivity between two signatures, using either the GSEA method based on the KS statistic, or the gwc method based on a weighted spearman statistic. The GSEA analysis is implemented in the piano package.
1 2 3  connectivityScore(x, y, method = c("gsea", "fgsea", "gwc"),
nperm = 10000, nthread = 1, gwc.method = c("spearman", "pearson"),
...)

x 
A 
y 
A 
method 

nperm 

nthread 

gwc.method 

... 
Additional arguments passed down to gsea and gwc functions 
numeric
a numeric vector with the score and the pvalue associated
with it
F. Pozzi, T. Di Matteo, T. Aste, "Exponential smoothing weighted correlations", The European Physical Journal B, Vol. 85, No 6, 2012. DOI: 10.1140/epjb/e201220697x
Varemo, L., Nielsen, J. and Nookaew, I. (2013) Enriching the gene set analysis of genomewide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Research. 41 (8), 43784391. doi: 10.1093/nar/gkt111
1 2 3 4 5 6 7 8  xValue < c(1,5,23,4,8,9,2,19,11,12,13)
xSig < c(0.01, 0.001, .97, 0.01,0.01,0.28,0.7,0.01,0.01,0.01,0.01)
yValue < c(1,5,10,4,8,19,22,19,11,12,13)
ySig < c(0.01, 0.001, .97,0.01, 0.01,0.78,0.9,0.01,0.01,0.01,0.01)
xx < cbind(xValue, xSig)
yy < cbind(yValue, ySig)
rownames(xx) < rownames(yy) < c('1','2','3','4','5','6','7','8','9','10','11')
data.cor < connectivityScore(xx,yy,method="gwc", gwc.method="spearman", nperm=300)

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