viperSimilarity {viper} | R Documentation |
If ws is a single number, weighting is performed using an exponential function. If ws is a 2 numbers vector, weighting is performed with a symmetric sigmoid function using the first element as inflection point and the second as trend.
viperSimilarity(x, nn = NULL, ws = c(4, 2), method = c("two.sided", "greater", "less"))
x |
Numeric matrix containing the VIPER results with samples in columns and regulators in rows |
nn |
Optional number of top regulators to consider for computing the similarity |
ws |
Number indicating the weighting exponent for the signature, or vector of 2 numbers indicating the inflection point and the value corresponding to a weighting score of .1 for a sigmoid transformation, only used if |
method |
Character string indicating whether the most active (greater), less active (less) or both tails (two.sided) of the signature should be used for computing the similarity |
This function computes the similarity between VIPER signatures
signatureDistance object
data(bcellViper, package="bcellViper") dd <- viperSimilarity(exprs(dset)) dd[1:5, 1:5] scale(dd)[1:5, 1:5] as.matrix(as.dist(dd))[1:5, 1:5]