Function to compute signature scores as linear combination of gene expressions

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Description

This function computes a signature score from a gene list (aka gene signature), i.e. a signed average as published in Sotiriou et al. 2006 and Haibe-Kains et al. 2009.

Usage

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sig.score(x, data, annot, do.mapping = FALSE, mapping, size = 0,
  cutoff = NA, signed = TRUE, verbose = FALSE)

Arguments

x

Matrix containing the gene(s) in the gene list in rows and at least three columns: "probe", "EntrezGene.ID" and "coefficient" standing for the name of the probe, the NCBI Entrez Gene id and the coefficient giving the direction and the strength of the association of each gene in the gene list.

data

Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined.

annot

Matrix of annotations with at least one column named "EntrezGene.ID", dimnames being properly defined.

do.mapping

TRUE if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene), FALSE otherwise.

mapping

Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance.

size

Integer specifying the number of probes to be considered in signature computation. The probes will be sorted by absolute value of coefficients.

cutoff

Only the probes with coefficient greater than cutoff will be considered in signature computation.

signed

TRUE if only the sign of the coefficient must be considered in signature computation, FALSE otherwise.

verbose

TRUE to print informative messages, FALSE otherwise.

Value

score

Signature score.

mapping

Mapping used if necessary.

probe

If mapping is performed, this matrix contains the correspondence between the gene list (aka signature) and gene expression data.

Author(s)

Benjamin Haibe-Kains

References

Sotiriou C, Wirapati P, Loi S, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, Buyse M, Piccart MJ and Delorenzi M (2006) "Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis", Journal of National Cancer Institute, 98:262-272

Haibe-Kains B (2009) "Identification and Assessment of Gene Signatures in Human Breast Cancer", PhD thesis at Universite Libre de Bruxelles, http://theses.ulb.ac.be/ETD-db/collection/available/ULBetd-02182009-083101/

Examples

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## load NKI data
data(nkis)
## load GGI signature
data(sig.ggi)
## make of ggi signature a gene list
ggi.gl <- cbind(sig.ggi[ ,c("probe", "EntrezGene.ID")],
  "coefficient"=ifelse(sig.ggi[ ,"grade"] == 1, -1, 1))
## computation of signature scores
ggi.score <- sig.score(x=ggi.gl, data=data.nkis, annot=annot.nkis,
  do.mapping=TRUE, signed=TRUE, verbose=TRUE)
str(ggi.score)

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