readHapMap {fbat}R Documentation

Import HapMap data

Description

Import HapMap data and convert it to pedigree format.

Usage

readHapMap(hapmapfile, race="CEU", skip = 2, comment.char = "&", quiet = FALSE)

Arguments

hapmapfile the hapmap file name
race can take values CEU, YRI, CHB, and JPT
skip first skip lines in the file hapmapfile will be skipped.
comment.char hapmapfile snp names contain the symbol # which is the comment command of R. So by default, we set comment.char as “&”.
quiet print intermediate results if quiet=FALSE.

Details

HapMap files are those snp files output by HapMap browsers.

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 1.4.0 Index]