PrbCor: Probe Level Correlation of Two Sets of Genomic Data

In xueyuancao/CCPROMISE: PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Probe Level Correlation of Two Sets of Genomic Data

Description

Compute Spearman correlation of all probe combination between two sets of genomic data within a gene.

Usage

PrbCor (geneSet, Edat, Mdat, EMlbl = c("Expr", "Methyl"), phdat, 
    pcut = 0.05) 

Arguments

geneSet	a gene set collection to annotate probes to gene
Edat	data frame of the first form of genomic data, such as gene expression data with row being probes and column being subjects. The column names should match the row names phdat
Mdat	data frame of the second form of genomic data, such as methylation data with row being probes and column being subjects. The column names should match the row names phdat
EMlbl	lablel of the genomic data, default=c("Expr", "Methyl") for Edat and Mdat
phdat	phenotype data with row being subjects and column being phenotype variables. The row names should match the column names of Edat and Mdat
pcut	p value cutoff to eliminate probe pairs that are not significantly correlated. Default is 0.05

Details

The function performs Spearman correlation for all probe pairs between two forms genomic data within each gene (Edat and Mdat) defined by gann. If a gene only has one form of genomic data, the other form is coded as NA. The function return a list of two components. See value for details.

Value

The output of the function is a list of length 2. The 2 components are as following:

res	spearman correlation result: a data frame with row for each probe pair with correlation p value < pcut and five columns; Gene: Gene names; EMlbl[1]: probe id in the first form data; EMlbl[2]: probe id in the second form data; Spearman.rstat: Spearman r statistics; Spearman.p: Spearman p value.
gen	Probe level data: a data frame with row for each probe pairs, first half of columns for first form genomic data and second half of columns for second form genomic data with sign reflecting the correlation of the probe pair.

Author(s)

Xueyuan Cao [e-mail], Stanley Pounds [e-mail]

See Also

CCPROMISE

Examples

  ## load exmplPhDat exmplEdat exmplMdat
  data(exmplESet)
  data(exmplMSet)
  data(exmplGeneSet)
  ## Perform canonical correlation test
 test1<- PrbCor(geneSet=exmplGeneSet, 
              Edat=exprs(exmplESet), 
              Mdat=exprs(exmplMSet), 
              EMlbl=c("Expr", "Methyl"), 
              phdat=pData(exmplESet))   
 

xueyuancao/CCPROMISE documentation built on May 6, 2023, 8:29 a.m.