At this point in our tutorial, we now discuss the issues presented when analyzing larger data sets. As our first step, we load a new, and much larger data set: "mouse.raw". This file describes 308 markers scored on 46 progeny of an F2 intercross between the Mouse strains Mus castaneous with Mus musculus (C57/BL-6). These markers span the 19 mouse autosomes at an average density of about one every 5 cM. Note that our previous data set is saved when we load a new one.
Upon loading the data, you see that MAPMAKER begins executing a long stream of commands. This is not entirely automatic behavior, in the sense that we explicitly told MAPMAKER to do this by supplying an "initialization file", named (in this case) "mouse.prep". (If MAPMAKER does not now start doing this, you must be missing this file. Unfortunately, you need it to proceed with this tutorial). In this initialization file we execute many commands to help configure MAPMAKER to this particular data set, including:
These steps can take anywhere from 5-30 minutes, depending on your computer. To learn how the commands in our initialization file work, you can look the commands up in the reference section following this tutorial. In addition, these issues are discussed in detail in the section on "Preparing data", included with this manual.
One remark we will make here is that, for the rest of this tutorial, we will be working with marker names rather than MAPMAKER-assigned numbers (that is, our initialization file contained the command "print names on"). Our naming convention for the mouse data set is that all markers are given 4 character names, starting with a letter then three digits. This format is not a requirement of MAPMAKER however.
18> prepare data mouse.raw save loaded data first? yes saving genotype data in file 'sample.data'... ok saving map data in file 'sample.maps'... ok saving two-point data in file 'sample.2pt'... ok saving traits data in file 'sample.traits'... ok preparing data from file 'mouse.raw'... ok F2 intercross data (46 individuals, 308 loci)... ok running initialization commands from file 'mouse.prep'...19> units cm the 'units' are now set to (Haldane) centimorgans.
20> centimorgan func haldane centimorgan function: Haldane
21> print names on 'print names' is on.
22> triple error detection on 'triple error detection' is on.
23> informativeness criteria 4.0 44 codominant Informativeness Criteria: min Distance 4.0, min #Individuals 44 (codominant markers only)
24> make chromosome chrom1 chrom2 chrom3 chrom4 chrom5 chrom6 chromosomes defined: chrom1 chrom2 chrom3 chrom4 chrom5 chrom6
25> make chromosome chrom7 chrom8 chrom9 chrom10 chrom11 chromosomes defined: chrom1 chrom2 chrom3 chrom4 chrom5 chrom6 chrom7 chrom8 chrom9 chrom10 chrom11
26> make chromosome chrom12 chrom13 chrom14 chrom15 chrom16 chromosomes defined: chrom1 chrom2 chrom3 chrom4 chrom5 chrom6 chrom7 chrom8 chrom9 chrom10 chrom11 chrom12 chrom13 chrom14 chrom15 chrom16
27> make chromosome chrom17 chrom18 chrom19 chromosomes defined: chrom1 chrom2 chrom3 chrom4 chrom5 chrom6 chrom7 chrom8 chrom9 chrom10 chrom11 chrom12 chrom13 chrom14 chrom15 chrom16 chrom17 chrom18 chrom19 .
<< More Output Follows .