make_GXM: Compute gene expression correlation matrix.
In vtrubets/OmicKriging: Poly-Omic Prediction of Complex TRaits

Description Usage Arguments Value Examples

View source: R/correlation_matrices.R

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.

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

`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.

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

## 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)