calculateCor {facopy} | R Documentation

## Calculate Correlation Between Copy Number and Expression

### Description

Calculates the gene-wise correlation between copy number and expression data, which might come from: (1) the `facopyInfo` object and user-provided expression data or (2) from an external database.

### Usage

    calculateCor(fad, exprProfile, db = NULL)

### Arguments

`fad` | `facopyInfo` object with a certain study's `facopy` data.
`exprProfile` | Either a character or a `data.frame`. If `db` is `NULL`, a `data.frame` with the expression data or a character that indicates the file with the expression data, with headers and tab-delimited. Otherwise, a character indicating the the name of the expression profile in the Cancer Genomics Data Server. See `http://www.cbioportal.org/public-portal/cgds_r.jsp`.
`db` | A character indicating the the name of the dataset, in the Cancer Genomics Data Server, from which to get the expression profile. See `http://www.cbioportal.org/public-portal/cgds_r.jsp`.

### Details

Only use this function and `facopyEnrichment` if you selected some kind of gene collection as genomic features.

### Value

The returned object is used to select genes in the enrichment process encapsulated in the `facopyEnrichment` function.

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

    eCor = calculateCor(myStudy, "mrna_merged_median_Zscores", "coadread_tcga_pub")
    head(eCor$cor)

[Package facopy version 1.13.0 Index]