sequoia (version 2.11.1)

LHConvert: Extract Sex and Birth Year from PLINK File

Description

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
)

Value

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

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.

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.

See Also

GenoConvert, PedStripFID to reverse UseFID.

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)
}