readGenes.pfizer {GeneticsBase}R Documentation

Read genetics data files that use Pfizer's data format.

Description

Read genetics data files that use Pfizer's data format.

Usage

readGenes.pfizer(filename, phase=list(F),
                 format=c("Pivot", "Listing"),...)

Arguments

filename Name of the file in which data is stored
phase see below
format Format of the file to be read, one of "Pivot" or "Listing"
... Additional arguments to function read.table

Details

The argument phase may be:

    1
    A single logical scalar value that applies for all markers
    2
    A logical vector with one element per marker
    3
    A phaseObject (TBD) providing observation by marker by phase probabilities + definitions of contigs + probability of contigs

Value

a geneSet object

Author(s)

Gregory R. Warnes warnes@bst.rochester.edu and Nitin Jain nitin.jain@pfizer.com

Examples


# store where we are now
here <- getwd()

# move to the data directory
dir <- file.path(.path.package("GeneticsBase"),"data")
setwd(dir)

# load Pfizer Data
PfizerExample <- readGenes.pfizer("PfizerExample.txt", format="Listing")

# look at the data
PfizerExample

# return to the original path
setwd(here)


[Package GeneticsBase version 1.2.0 Index]