readGenes {GeneticsBase} | R Documentation

## Import genetic data from standard file formats

### Description

Import genetic data from standard file formats.

### Usage

    readGenes(gfile, gformat=genotypeFileFormats,  goptions=list(),
              pfile, pformat=phenotypeFileFormats, poptions=list(),
              mfile, mformat=markerFileFormats,    moptions=list() )

### Arguments

`gfile` | File containing genotype data
`gformat` | Function, function name, or a character file format specification from the list `genotypeFileFormats`.
`goptions` | Optional arguments for loading genotype data.
`pfile` | File containing phenotype data
`pformat` | Function, function name, or a character file format specification from the list `phenotypeFileFormats`.
`poptions` | Optional arguments for loading phenotype data.
`mfile` | File containing marker data
`mformat` | Function, function name, or a character file format specification from the list `markerFileFormats`.
`moptions` | Optional arguments for loading marker data.

### Details

Load genotype and (optionally) phenotype and marker information from the specified files and generate a geneSet object containing the results.

A variety of file formats are available. See the variables `genotypeFileFormats`, `phenotypeFileFormats`, `phenotypeFileFormats` for formats.

### Value

An object of class geneSet.

### Note

Adding a new genotype (phenotype) file format requires creation of a function named `readGenes.newformat` (`read.newformat`) and adding the string "newformat" to the vector `genotypeFileFormats` (`phenotypeFileFormats`).

Please submit new format functions to the authors for inclusion in the package.

### Author(s)

Gregory R. Warnes warnes@bst.rochester.edu

### See Also

`read.table`, etc

### Examples

    # Perlegen data set (if we have access to it)
    # (189K SNPS x 1008 patients)
    path <- "~/clingen/Perlegen_Metabolic_Disorder/Data"
    fname <- file.path(path,"PFZ_03/genotype.txt.gz")
    if(file.exists(fname))
      {
        genef   <- gzfile(fname) # open the gzip compressed SNP file
        #phenof  <-
        markerf <-file.path(path,"PFZ_03/snp_info.txt")

        pgdata <- readGenes(gfile=genef, gformat="perlegen",
                            mfile=markerf, mformat="table",
                            moptions=list(sep="\t",header=TRUE))
        close(genef)
      }

[Package GeneticsBase version 1.6.0 Index]