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 1.2.0 Index]