createArrayData {cpvSNP} | R Documentation

## 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.

### Details

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

### Value

A GRanges object.

### Author(s)

Jason Hackney, Jessica Larson, Caitlin McHugh mchughc@uw.edu

### Examples

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

[Package cpvSNP version 1.12.0 Index]