make_GXM: Compute gene expression correlation matrix.

In hakyimlab/OmicKriging: Poly-Omic Prediction of Complex TRaits

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

expFile	Path to gene expression file.
gxmFilePrefix	File path prefixes for outputting GCTA style binary correlation matrices.
idfile	Path to file containing family IDs and sample IDs with header FID and IID.

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)

hakyimlab/OmicKriging documentation built on Nov. 1, 2020, 1:33 a.m.