Sib-pair Command: write

Class	Analysis and data manipulation command
Name	write
Arguments	[<pedigree file name>]

Writes a GAS type pedigree file from the current dataset. Default is to screen. Note that this command respects the set printstyle <mask> command, where the mask controls whether or not each of the first five fields are printed, the set gen command (sets the allele separator for writing genotypes), and the set mis (sets the missing data token).

Example:

>> set loc q1 qua
>> set loc m1 mar
>> read pedigree inline
ped1 Bob Mark Alice m 10 a/b
;;;;
>> run
>> write
 Writing  1  pedigrees:
!
!                     S
!                     e
!Ped Perso Fath Mothe x    q1       m1
!
ped1 Alice x    x     f     x       x/x
ped1 Mark  x    x     m     x       x/x
ped1 Bob   Mark Alice m   10.0000   a/b

>> set printstyle 01001
>> set missing .
>> set genotype_separator " "
>> write

Writing 1 pedigrees:
!     S
!     e
! Per x    q1       m1
!
 Alice f     .       . .
 Mark  m     .       . .
 Bob   m   10.0000   a b

See also:

print	print data where expression true
set printstyle	output style for print command
set gen	allele separator for writing genotypes
set mis	set missing data token for printing

Sib-pair Command: write

Class	Analysis and data manipulation command
Name	write
Arguments	<format>	<pedigree file name>	<modifier>
	pedigree|gas		[header]
	arl		[par|all]
	asp|fbat|tcl		[dummy]
	crimap
	csv		[nop]
	dot
	fisher
	gda		[all]
	haploview
	linkage|ppd|gh		[dummy] [numbered_alleles]
	mendel
	merlin		[dummy]
	phe
	sage
	solar		[phe|gen] [nopedigreeID]

The write command writes the current dataset to a file in the format used by a variety of other programs for genetic analysis. Quantitative values are written as Fw.d (default F9.4 , see set ndecimal) or F8.4 (for programs such as MENDEL).

Use of the keywords pedigree or gas writes a GAS type pedigree file from the current dataset. If the header modifier keyword is present, then a line of the variable names is prepended.

The keyword gda writes a GDA Nexus datafile containing all current marker genotypes for founders. If the keyword all is added, nonfounders will be included as well, but the "gdatype" format will not differentiate between relatives.

Similarly, arlequin writes a data file for the program Arlequin containing haplotypes from one informative child per family, or two parents of such a child if the par keyword is added. Only if the all keyword is added will all genotyped individuals be printed.

The keywords linkage and ppd write a pedigree file from the current dataset suitable for use by the LINKAGE (and FASTLINK) programs, the former type requires preprocessing by the Makeped program (note that if a quantitative trait value is zero -- that is nonmissing -- it is recoded to 0.0001);

aspex, fbat, or tcl, writes a linkage style pedigree file but with the marker locus names as the first line, as the ASPEX programs prefer;

gh writes a linkage style pedigree file with a dummy affection trait as the first trait and all the quantitative traits last, with "-" for missing quantitative trait values. The dummy option added to linkage or gh writes a dummy affection locus as the the first trait (everybody affected). The numbered_allele option skips recoding alleles to numbered alleles.

The haploview option is a linkage style file with recoding of letter alleles from "ACGT" to "1234".

merlin writes a pedigree file suitable for Merlin -- actually a LINKAGE "pre" format file with zygosity included as the first trait, if the "set twin" command has been previously issued;

The sage keyword writes a pedigree file from the current dataset suitable for use by the program FSP included in the SAGE package.

The mendel keyword writes a pedigree file from the current dataset suitable for use by the programs MENDEL or SIMWALK; fisher writes a pedigree file from the current dataset suitable for use by the related program FISHER.

phe writes the "pheno.dat" style file required by Mapmaker-Sibs;

cri writes the ".gen" style file required by CRI-MAP;

Both csv and solar give a comma delimited file, with header naming columns, from which the pedigree ID column can be dropped via the nop option, and the SOLAR phenotype (or genotype) file written by the phe (gen) option. The SOLAR pedigree file has two additional columns: MZ twin indicator (requiring a previous "set twin") and a household (actually pedigree) indicator.

The structure and beagle commands write genotype data files for Structure and Beagle respectively (and can be restricted to writing just founder data using the founders option).

Example:

>> write csv lincl.csv

See also:

set liability	Declare a quantitative trait to be a liability class indicator
write locus	Write a locus file