Compute gene expression correlation matrix.

Description

This function computes a gene expression correlation matrix given a file of transcript expression levels for each sample in the study. It returns a correlation matrix with rownames and colnames as sample IDs.

Usage

make_GXM(expFile = NULL, gxmFilePrefix = NULL, idfile = NULL)

Arguments

Value

Returns a correlation matrix of (N-samples x N-samples), with rownames and colnames as sample IDs.

Examples

 ## load gene expression values from vignette
 expressionFile <- system.file(package = "OmicKriging",
                     "doc/vignette_data/ig_gene_subset.txt.gz")
 ## compute correlation matrix
 geneCorrelationMatrix <- make_GXM(expressionFile)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OmicKriging)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/OmicKriging/make_GXM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: make_GXM
> ### Title: Compute gene expression correlation matrix.
> ### Aliases: make_GXM
> 
> ### ** Examples
> 
>  ## load gene expression values from vignette
>  expressionFile <- system.file(package = "OmicKriging",
+                      "doc/vignette_data/ig_gene_subset.txt.gz")
>  ## compute correlation matrix
>  geneCorrelationMatrix <- make_GXM(expressionFile)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>