Class | Global |
Name | summary |
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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