Sib-pair Command: summary


ClassGlobal
Namesummary
Arguments[<N highest results> | plot [qq] [<EPS file>] | table] .

If the plot keyword is issued, a Postscript plot of the -log10 P-values versus map position of the active marker loci tested for association or linkage in the last analysis, unless the qq modifier keyword is present. In that case, a quantile-quantile plot of the -log10 P-values is produced. This is saved to a file (default name "sib-pair.eps").

For the table modifier keyword, a table of binned P-values or test statistics is produced; usual bin sizes are powers of ten.

Example:

>> include cavanaughex.in
>> apm ibd
>> summary

Test: "apm ibd".

Total number of tests =      8

Locus          Position  P-value   -log10(P)
-------------- --------- -------  ----------
D16S411            62.23  5e-12       11.286  48294236 (chr 16)
D16S409            61.00  0.0027       2.571  47333369 (chr 16)
D16S753            60.12  0.0027       2.562  31181005 (chr 16)
D16S3145           55.01  0.0036       2.446  26784604 (chr 16)
D16S419            67.69  0.0082       2.087  51510863 (chr 16)

>> summary 10

Locus          Position   P-value   -log10(P)
-------------- ---------- -------  ----------
D16S411             62.23  5e-12       11.286  48294236 (chr 16)
D16S409             61.00  0.0027       2.571  47333369 (chr 16)
D16S753             60.12  0.0027       2.562  31181005 (chr 16)
D16S3145            55.01  0.0036       2.446  26784604 (chr 16)
D16S419             67.69  0.0082       2.087  51510863 (chr 16)
D16S415             69.15  0.0483       1.316  52228236 (chr 16)
D16S771             70.85  0.1120       0.951  53066505 (chr 16)
D16S769             53.71  0.1297       0.887  26066263 (chr 16)


>> summary tab

Bin     Count  Percent
------- -----  -------
10^-11      1    12.5
10^-8       0     0.0
10^-7       0     0.0
10^-6       0     0.0
10^-5       0     0.0
10^-4       0     0.0
10^-3       0     0.0
10^-2       4    50.0
10^-1       1    12.5
10^0        2    25.0


>> summary plot
>> $ gv sib-pair.eps &

Resulting plot:


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