MAMA (version 2.2.1)

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, the rownames in the gene expression data matrices must be equal

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)

B

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:

ordering

Ordered Gene Lists as a data.frame where columns refer to datasets

alpha.selected

Selected value of alpha parameter

alpha.considered

Vector of alpha considered for selection

pAUC

pAUC values related to all alphas considered

random

Random scores (permutations of class labels)

subsample

Scores after subsampling from each class and dataset

emp.ci

Empirical confidence intervals for number of overlapping genes

common.genes

Vector of number of overlapping genes

score

Observed similarity score

significance

Significance of the observed score in form of p-value

genes

Genes that account for observed similarity score

all.genes

Names of the all genes in the analysis

References

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