readGenes {GeneticsBase} | R Documentation |
Import genetic data from standard file formats.
readGenes(gfile, gformat=genotypeFileFormats, goptions=list(), pfile, pformat=phenotypeFileFormats, poptions=list(), mfile, mformat=markerFileFormats, moptions=list() )
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. |
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.
An object of class geneSet.
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.
Gregory R. Warnes warnes@bst.rochester.edu
read.table
, etc
# 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) }