tpacForCollection | R Documentation |
Executes the TPAC (tissue-adjusted pathway analysis for cancer) method (tpac
) on multiple gene sets, i.e., a gene set collection.
tpacForCollection(gene.expr, mean.expr, tissue.specificity, gene.set.collection)
gene.expr |
See description in |
mean.expr |
See description in |
tissue.specificity |
See description in |
gene.set.collection |
List of m gene sets for which scores are computed.
Each element in the list corresponds to a gene set and the list element is a vector
of indices for the genes in the set. The index value is defined relative to the
order of genes in the |
A list containing two elements:
s.pos
: n x m matrix of TPAC scores computed using the positive squared adjusted Mahalanobis distances.
s.neg
: n x m matrix of TPAC scores computed using the negative squared adjusted Mahalanobis distances.
s
: n x m matrix of TPAC scores computed using the sum of the positive and negative squared adjusted Mahalanobis distances.
tpac
,tpacForCancer
# Simulate Gaussian expression data for 10 genes and 10 samples
gene.expr=matrix(rnorm(100), nrow=10)
# Use 0 as mean.expr
mean.expr=rep(0,10)
# Simulate tissue-specific weights
tissue.specificity = runif(10, min=0.5, max=1.5)
# Define a collection with two disjoint sets that span the 10 genes
collection=list(set1=1:5, set2=6:10)
# Execute TPAC on both sets
tpacForCollection(gene.expr=gene.expr, mean.expr=mean.expr,
tissue.specificity=tissue.specificity, gene.set.collection=collection)
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