performSOGL: Function to perform analysis using Similarity of Ordered Gene Lists

Description

This a wrapper function to perform all steps designed in Similarity of Ordered Gene Lists.

Usage

performSOGL(data, varname, test, B, which = c("score", "empirical"), min.weight = 1e-05, two.sided = TRUE, percent = 0.95)

Arguments

data

MetaArray object

varname

A string indicating which column of clinical data matrices should be used to compute test statistic. Same column is used in all datasets.

test

"FCH" for fold change (function fold.change) or "T" for T-test (function meta.test)

Number of permuatations

which

if "empirical" then empirical confidence intervals of number of overlapping genes are also provided, if "score" only random and subsampled scores necessary for tunning alpha parameter are calculated

min.weight

Minimal weight for score calculation

two.sided

if TRUE both top and bottom of the ordered gene lists are considered, if FALSE only top ones

percent

Percentage (Numeric between 0 and 1) of the score for genes selection

Value

Object of class SOGLresult, it is a list containig:
orderingOrdered Gene Lists as a data.frame where columns refer to datasets
alpha.selectedSelected value of alpha parameter
alpha.consideredVector of alpha considered for selection
pAUCpAUC values related to all alphas considered
randomRandom scores (permutations of class labels)
subsampleScores after subsampling from each class and dataset
emp.ciEmpirical confidence intervals for number of overlapping genes
common.genesVector of number of overlapping genes
scoreObserved similarity score
significanceSignificance of the observed score in form of p-value
genesGenes that account for observed similarity score

References

Yang, X., Bentink, S., Scheid, S. Spang, R., Similarities of ordered gene lists, 2005