convertToDr {RTopper} | R Documentation

## 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

### 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.

### Value

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

### Author(s)

Luigi Marchionni marchion@jhu.edu

### 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)

[Package RTopper version 1.28.0 Index]