readHapMap {fbat} | R Documentation |
Import HapMap data and convert it to pedigree format.
readHapMap(hapmapfile, race="CEU", skip = 2, comment.char = "&", quiet = FALSE)
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 . |
HapMap files are those snp files output by HapMap browsers.
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.
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