calculateCor: Calculate Correlation Between Copy Number and Expression

In facopy: Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

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)

facopy documentation built on May 2, 2018, 2:30 a.m.