gsea.iriz {nethet} | R Documentation |
Irizarry approach for gene-set testing
gsea.iriz(x1, x2, gene.sets, gene.names, gs.names = NULL, method.p.adjust = "fdr", alternative = "two-sided")
x1 |
Expression matrix (condition 1) |
x2 |
Expression matrix (condition 2) |
gene.sets |
List of gene-sets |
gene.names |
Gene names |
gs.names |
Gene-set names |
method.p.adjust |
Method for p-value adjustment (default='fdr') |
alternative |
Default='two-sided' (uses two-sided p-values). |
Implements the approach described in "Gene set enrichment analysis made simple" by Irizarry et al (2011). It tests for shift and/or change in scale of the distribution.
List consisting of
pval.shift |
p-values measuring shift |
pval.scale |
p-values measuring scale |
pval.combined |
combined p-values (minimum of pval.shift and pval.scale) |
n.stadler
n <- 100 p <- 20 x1 <- matrix(rnorm(n*p),n,p) x2 <- matrix(rnorm(n*p),n,p) gene.names <- paste('G',1:p,sep='') gsets <- split(gene.names,rep(1:4,each=5)) fit <- gsea.iriz(x1,x2,gsets,gene.names) fit$pvals.combined x2[,1:3] <- x2[,1:3]+0.5#variables 1-3 of first gene-set are upregulated fit <- gsea.iriz(x1,x2,gsets,gene.names) fit$pvals.combined