read.linkdat: Read/write 'linkdat' objects

Description

Create 'linkdat' object from a pedigree file with simulation and/or marker information (e.g. pre-makeped format).

Usage

read.linkdat(file, header = FALSE, simcol = NA, missing=0, 
             model=NULL, ...)

write.linkdat(x, file="", col.names=FALSE, famid=TRUE)

Arguments

file

the name of the file containing the pedigree. See Details for format information.

a code{linkdat} object.

header

a logical value indicating whether the file contains column names. If TRUE, the names of columns 1-5 (or 2-6 if famid=TRUE) must be ID, FID, MID, SEX and AFF in this order.

famid

a logical value indicating whether the first column of the output file should be a family id, consisting of all 1's. (This makes the file of classical LINKAGE format, hence compatible with other linkage software.) If header=TRUE the column

simcol

an integer indicating the column (if present) containing simulation statuses. Not necessary if header=TRUE and the header of the simulation column is SIM.

missing

a numeric or character of length 1 indicating the code for missing marker alleles.

model

optional: the linkage model to be passed onto setModel (see this for details).

col.names

a logical value indicating if column names should be included in the file.

...

further arguments to be passed to read.table.

Value

For read.linkdat, a linkdat object.

Details

The columns should be: Family id (optional); individual id; father id; mother id; sex; affection status; simulation status (optional); marker1_allel1; marker1_allel2; a.s.o. If the file includes headers, these must be ('FAMID'), 'ID', 'FID', 'MID', 'SEX', 'AFF' and 'SIM'. Marker column names are ignored. If the file has no headers, the program looks for a family id column by checking if the numbers in the first column are all equal. If this is found to be true, a statement to this effect is printed and the column is removed.

Examples

Run this code

data(toyped)
toy=linkdat(toyped, model=1)
write.linkdat(toy, "toy.ped", col.names=TRUE)
toy2=read.linkdat("toy.ped", header=TRUE)
toy2
write.linkdat(toy, "toy_famid.ped") 
toy3=read.linkdat("toy_famid.ped")
toy3