Mergeomics (version 1.0.0)

tool.normalize.quality: Check normalization quality

Description

tool.normalize.quality checks transformation quality by using Kolmogorov-Smirnov Test. It seeks the best log transform parameter within the previously specified upper and lower limits, and applies the log transform with the best log parameter.

Usage

tool.normalize.quality(g, z)

Arguments

g

normalization quality control will take place according to the normal distribution parameters defined by g, e.g. it can be normal distribution with 0-mean and std dev 1.

z

transformed data, i.e. either p-value or enrichment score

Value

res

statitics of Kolmogorov-Smirnov Test result obtained for z values

See Also

tool.normalize

Examples

set.seed(1)
## let us assume we have a set of normalized scores: 
z <- abs(rnorm(10)) ## it should be positive and at least 10 length-vector
z <- z/median(z)
## Find the best log transform.
gamma <- optim(par=1.0, fn=tool.normalize.quality, gr=NULL, z,
lower=-9, upper=9, control=list(reltol=1e-3))
## After finding the best log transform, apply transform:
z <- log(exp(gamma$par)*z + 1.0)