Extract Sex and Birth Year from PLINK File

Convert the first six columns of a PLINK .fam, .ped or .raw file into a three-column lifehistory file for sequoia. Optionally FID and IID are combined.

Usage

LHConvert(
  PlinkFile = NULL,
  UseFID = FALSE,
  SwapSex = TRUE,
  FIDsep = "__",
  LifeHistData = NULL
)

Arguments

PlinkFile: character string with name of genotype file to be converted.
UseFID: use the family ID column. The resulting ids (rownames of GenoM) will be in the form FID__IID.
SwapSex: change the coding from PLINK default (1=male, 2=female) to sequoia default (1=female, 2=male); any other numbers are set to NA.
FIDsep: characters inbetween FID and IID in composite-ID. By default a double underscore is used, to avoid problems when some IIDs contain an underscore. Only used when UseFID=TRUE.
LifeHistData: dataframe with additional sex and birth year info. In case of conflicts, LifeHistData takes priority, with a warning. If UseFID=TRUE, IDs in LifeHistData are assumed to be already as FID__IID.

Value

A dataframe with id, sex and birth year, which can be used as input for sequoia.

Details

The first 6 columns of PLINK .fam, .ped and .raw files are by default FID - IID - father ID (ignored) - mother ID (ignored) - sex - phenotype.

Examples

if (FALSE) {
# combine FID and IID in dataframe with additional sex & birth years
ExtraLH$FID_IID <- paste(ExtraLH$FID, ExtraLH$IID, sep = "__")
LH.new <- LHConvert(PlinkFile, UseFID = TRUE, FIDsep = "__",
                    LifeHistData = ExtraLH)
}