Description Usage Arguments Value Author(s) References
This a wrapper function to perform all steps designed in Similarity of Ordered Gene Lists.
1  performSOGL(data, varname, test, B, which = c("score", "empirical"), min.weight = 1e05, two.sided = TRUE, percent = 0.95)

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 

B 
Number of permuatations 
which 
if 
min.weight 
Minimal weight for score calculation 
two.sided 
if 
percent 
Percentage (Numeric between 
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 pvalue 
genes 
Genes that account for observed similarity score 
all.genes 
Names of the all genes in the analysis 
Ivana Ihnatova
Yang, X., Bentink, S., Scheid, S. Spang, R., Similarities of ordered gene lists, 2005
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.