readLink {fbat} | R Documentation |
Import file with PLINK data format and convert it to a pedigree object.
readLink(pedfile, gmfile, columns = c("family", "pid", "father", "mother", "sex"), quiet = FALSE)
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 . |
The data format is used by the software PLINK.
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