Sib-pair Command: write locus


ClassAnalysis and data manipulation command
Namewrite locus
Arguments<type> <file> [<arg>]
aspex|tcl <locus file name>
beagle
fisher
gas
haploview
linkage|gh[dummy] [xlinked]
loki [<pedigree file name>]
mendel [trait]
merlin
relpair
sage [par]
sib-pair [<pedigree file name>]
structure [<pedigree file name>]
superlink [dummy] [xlinked]

Use of the keyword gas writes a GAS type locus file from the current dataset;

haploview writes an "info" file, giving the marker position as the first word of the annotation if it is numerical, or the map position multiplied by 106;

linkage writes a locus file from the current dataset suitable for use by the LINKAGE (and FASTLINK) programs; gh writes the same as linkage save that map distances are in cM. The dummy option is used when the first trait is a dummy trait generated by

write linkage <file> dummy
while the xlinked option declares the markers to be all X-linked.

The keyword loki writes a control file for LOKI's prep program;

sage writes a locus file from the current dataset suitable for use by the SAGE package, or a parameter file (if the par modifier is present) as used by the more recent SAGE programs;

mendel writes a locus file from the current dataset suitable for use by the programs MENDEL or SIMWALK (with binary traits defaulting to a factor, but given as a diallelic locus if the trait modifier is present);

fisher writes a locus file from the current dataset suitable for use by the program FISHER;

merlin for MERLIN;

tcl or aspex writes the tcl command file required by ASPEX programs such as SIB_PHASE;

sib-pair writes a Sib-pair style script;

superlink writes a LINKAGE style locus file modified for the SUPERGH option of SUPERLINK;

relpair writes the RELPAIR format (modified from that for MENDEL): it infers chromosome number from the map position (as multiples of 1000) or from the locus name (if it takes the form of "DxSxxx").

structure writes the mainparams file required by the STRUCTURE program.

beagle writes a Beagle marker file: each record is the marker name, position (bp), allele names.

Example:

write locus merlin merlin.dat

See also:

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


<< (write pap)Up to index>> (write locus pap)