Ztrim.pl reads from the standard input and writes to the standard
output. It reads the output of Zmapqtl and eliminates columns based on
the value of Hypothesis. It is a quick way to make the output file fit
in a terminal window without having the text wrap.

This option requires an integer value greater than 1. It specifies how often the column headers should
be printed. The default value of 0 means that headers will be printed at the top of
each block of output. If your terminal shows 25 lines, then it is useful to reprint the header every
21 lines so as to have a header on each page of the output. (The header is 3 lines long...if you use
more, then you will need one more line for it.)

This option requires an integer value greater than 1. It specifies character width of
the output terminal. The default is 80, which is a common value. It only effects the
horizontal bars defining the headers.

Different values used with the -H option allow the user to output
specific columns from the qtlcart.z file. All options print out
columns for the chromosome, marker and postions. All print at least one
likelihood ratio test statistic and at least one parameter estimate.

For crosses with two marker classes (backcrosses and recombinant inbreds),
we can estimate one parameter value, namely the additive effect. The test is
H0 (no QTL) versus H1 (QTL with an additive effect a).

For crosses with three marker classes, we can estimate additive and dominance effects.
Let a be the additive effect and d be the dominance effect.
We can set up four hypotheses:

QTL with both an additive and a dominance effect: a not 0 and d not 0.
We refer to the estimate of
the additive effect as a3 and that of the dominance effect as d3 under this hypothesis.

Using the following values with the -H option yields

This is the default and is useful for crosses with two genotypic classes.
The output simply deletes the columns with zeros. You are left with the
likelihood ratio of H1 to H0 and the estimate of the additive effect.

This essentially prints the same information as 1 above except it does it for
crosses with three genotypic classes.

This prints the likelihood ratio for a test of dominance where the additive effect is zero.
You get the H2 to H0 likelihood ratio, the estimate of dominance, the R squared estimates and
the test statistic for normality of the residuals.

This prints the H3 to H0 likelihood ratio.
You get the hypothesis test likelihood ratio, the estimates of additivity and
dominance, the R squared estimates and
the test statistic for normality of the residuals.

This option prints everything that option 30 prints, but adds the test of H3 to H1 and
the a1 estimate.

This option prints everything that option 30 prints, but adds the test of H3 to H2 and
the d2 estimate.

will print the test statistic H3:H0 and the estimates of the additive and
dominance effects for the results in qtlcart.z. It will also reprint the
column headers every 20 lines. This works well for a terminal set to 24 lines
by 80 columns. The headers take 3 lines each and the more command chews up the
last line of each screen.

Christopher J. Basten, B. S. Weir and Z.-B. Zeng
Department of Statistics, North Carolina State University
Raleigh, NC 27695-7566, USA
Phone: (919)515-1934