RTopper (version 1.12.0)

convertToDr: Converts genomic data to a list suitable for computing gene-to-phenotype scores

Description

convertToDr converts genomic data into a list further used for computing gene-to-phenotype association scores.

Usage

convertToDr(dataIntersection, response, nPlatforms = length(data))

Arguments

dataIntersection

a list of data.frames containing genomic measurements. Each element of dataIntersection must account for the same set of patients(columns) and genes (rows)

response

a data.frame indicating patients' phenotypic class

nPlatforms

numeric, the number of genomic platforms

Value

A list of data.frames, one for each analyzed gene, summarizing all genomic measurements and phenotipic information across patients and platforms.

Details

This function coverts a list of data.frames containing distinct genomic measurtements performed on the same patients into a gene-centered used in further analyses for computing gene-to-phenotype scores. Data.frame in the input list (dataIntersection) must have the same dimentions, with columns being patients, and rows being genes. Column names identify the patients, while rownames identify the genes. The argument response is used to pass phenotypic information about samples to be analyzed. This is a simple two columns data.frame in which the first column correspond to patients identifiers, and the second column to the phenotypic response encoded as binary class (using the integers 0 and 1). The nPlatforms argument specifies the number of platforms that will be analyzed.

References

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin,and Giovanni Parmigiani "Integrating diverse genomic data using gene sets." Manuscript submitted.

Examples

###load data
data(exampleData)

###convert
dataDr <- convertToDr(dat, pheno, 4)