readLink {fbat}R Documentation

Import file with PLINK data format

Description

Import file with PLINK data format and convert it to a pedigree object.

Usage

readLink(pedfile, gmfile, columns = c("family", "pid", "father", "mother", "sex"), quiet = FALSE)

Arguments

pedfile pedigree data file with no marker info
gmfile marker info files. It contains three columns: marker IDs, marker names, and marker positions
columns By default, the first five columns of pedfile are sample information: family id, patient id, father id, mother id, patient sex.
quiet print intermediate results if quiet=FALSE.

Details

The data format is used by the software PLINK.

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.

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


[Package fbat version 1.6.0 Index]