readPed {fbat}R Documentation

Import pedigree file from standard pedigree file format

Description

Import pedigree file from standard pedigree file format.

Usage

readPed (
        filename,
        columns=c("family", "pid", "father", "mother",
                  "sex", "affected"),
        quiet=FALSE
        )

Arguments

filename File containing genotype data
columns column names for sample info
quiet indicates if intermediate output should be printed

Details

Value

A list with five elements: ped, columns, markerNames, Position, and fileName. ped is a pedigree data frame whose first 6 columns are family (pedigree id), pid (patient id), father (father id), mother (mother id), sex, affected (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual; columns are the names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother","sex","affected") or equal to c("family","pid","father","mother","sex"); founderOnly indicates if using only founder info; markerNames is a vector of marker names; Position is a vector of marker positions; fileName is the pedigree file name.

Note

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu, Gregory Warnes warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

See Also

read.table, etc

Examples






[Package fbat version 1.2.0 Index]