cpvSNP (version 1.4.0)

createArrayData: Create a GRanges Object for a GWAS data.frame

Description

Creates a GRanges object used for SNP set analysis.

Usage

createArrayData(arrayData, positionName = NULL, chromosomeName = "chromosome", chromosomeNameConvention = "NCBI", verbose = TRUE)

Arguments

arrayData

A data.frame containing array data from which the GRanges object will be created. This object is expected to include the position and chromosome, along with a SNP identifier and corresponding p-value.

positionName

The name of the column in the filepathData object that holds position data for each probe. By default, this value is NULL and there are columns Start and End which hold this information.

chromosomeName

The name of the column in the filepathData object that holds chromosome data for each probe. By default, this value is chromosome.

chromosomeNameConvention

The naming convention used for the chromosomes, either NCBI (default), UCSC, or a user specified mapping. By default, this is NCBI, indicating the autosomes are stored as integers and the mitochondrial and sex chromosomes are stored as MT and X, Y, respectively. The UCSC naming convention appends "chr" to each chromosome, and the mitochondrial coding is "chrM." Alternatively, a user can supply the mapping from each chromosome to the UCSC naming convention in the form of a character vector where the elements are the UCSC names and the corresponding names of the elements are the current chromosome names. An `NA' chromosome will be mapped to unknown. For more information, please see the GenomeInfoDb BioConductor R package.

verbose

A logical argument indicating whether output should be printed. The default is FALSE.

Value

A GRanges object.

Details

This function takes a data.frame and creates a GRanges object used for SNP set analysis.

Examples

    data(geneSetAnalysis)
    head(geneSetAnalysis$arrayData)
    arrayDataGR <- createArrayData(geneSetAnalysis[["arrayData"]], positionName="Position")