GlobalAncova (version 3.40.0)

GlobalAncova.decomp: GlobalAncova with sequential and type III sum of squares decomposition and adjustment for global covariates

Description

Computation of a F-test for the association between expression values and clinical entities. The test is carried out by comparison of corresponding linear models via the extra sum of squares principle. In models with various influencing factors extra sums of squares can be treated with sequential and type III decomposition. Adjustment for global covariates, e.g. gene expression values in normal tissue as compared to tumour tissue, can be applied. Given theoretical p-values may not be appropriate due to correlations and non-normality. The functions are hence seen more as a descriptive tool.

Usage

GlobalAncova.decomp(xx, formula, model.dat = NULL, method = c("sequential", "type3", "all"),  test.genes = NULL, genewise = FALSE, zz = NULL, zz.per.gene = FALSE)

Arguments

xx

Matrix of gene expression data, where columns correspond to samples and rows to genes. The data should be properly normalized beforehand (and log- or otherwise transformed). Missing values are not allowed. Gene and sample names can be included as the row and column names of xx.

formula

Model formula for the linear model.

model.dat

Data frame that contains all the variable information for each sample.

method

Whether sequential or type III decomposition or both should be calculated.

test.genes

Vector of gene names or a list where each element is a vector of gene names.

genewise

Shall the sequential decomposition be displayed for each single gene in a (small) gene set?

zz

Global covariate, i.e. matrix of same dimensions as xx.

zz.per.gene

If set to TRUE the adjustment for the global covariate is applied on a gene-wise basis.

Value

• Depending on parameters test.genes, method and genewise ANOVA tables, or lists of ANOVA tables for each decomposition and/or gene set, or lists with components of ANOVA tables for each gene are returned.

See Also

Plot.sequential, pair.compare, GlobalAncova

Examples

data(vantVeer)
data(phenodata)
data(pathways)

# sequential or type III decomposition
GlobalAncova.decomp(xx = vantVeer, formula = ~ grade + metastases + ERstatus, model.dat = phenodata, method = "sequential", test.genes = pathways[1:3])
GlobalAncova.decomp(xx = vantVeer, formula = ~ grade + metastases + ERstatus, model.dat = phenodata, method = "type3", test.genes = pathways[1:3]) 

# adjustment for global covariate
data(colon.tumour)
data(colon.normal)
data(colon.pheno)
GlobalAncova.decomp(xx = colon.tumour, formula = ~ UICC.stage + sex + location, model.dat = colon.pheno, method = "all", zz = colon.normal)