GEDI: Gene Expression and Dosage Integrator

In cghRA: Array CGH Data Analysis and Visualization

Description

This function implements the "Gene Expression and Dosage Integrator" CGH / transcriptome correlation, as described by Lenz et al.

Usage

  GEDI(cgh, cgh.chrom, cgh.start, cgh.end, cgh.genes, expr, expr.genes,
    permutations = 1000, type = c("amplifications", "deletions"), quiet = FALSE)

Arguments

cgh	Logical matrix, with regions in rows and samples in columns. Alterated samples for a given region are to be TRUE, germline FALSE and other NA.
cgh.chrom	Character vector, the chromosome location of the regions described in cgh.
cgh.start	Integer vector, the starting position on the chromosome for the regions described in cgh.
cgh.end	Integer vector, the ending position on the chromosome for the regions described in cgh.
cgh.genes	Character vector, the names of the genes in each region described in cgh, separated by ", ". See the cross method of the sliceable class (in Rgb package) for an easy way to produce this, in combination with track.NCBI_genes.
expr	Numeric matrix of gene expressions, with probesets in rows and samples in columns.
expr.genes	Character vector, the names of the genes associated with each probeset described in expr, separated by ", ". Notice probesets associated with multiple genes will not be used, as they are not specific.
permutations	Single integer value, the amount of permutations to use for score computation. Time consumption and score accuracy increases with this value.
type	Single character value, describing the type of alterations studied (as the alternative hypothesis for the t-test depends on it).
quiet	Single logical value, when FALSE a message will be sent for each region processing, in order to evaluate the processing time.

Value

Returns a list with the following elements :

gediScore	Numeric vector with for each cgh row the proportion of permutated scores lesser than the observed one. The algorithm authors consider an association to be present if this score is greater than 0.9.
gediGenes	Character vector with for each cgh row the list of the genes used for the score computation (intersection of cgh.genes and expr.genes for the considered region).

Author(s)

Sylvain Mareschal

References

Lenz G et al. "Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways". Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13520-5 (Supporting Information)

cghRA documentation built on May 2, 2019, 3:34 a.m.