| Class | Analysis and data manipulation command |
| Name | apm |
| Arguments | <binary trait>|(<quantitative trait> >|>=|<|<=|==|^= <threshold>) [ibd|ibs] |
Prints APM statistics for all marker loci versus the trait.
Example:
>> apm AD
------------------------------------------------
APM for trait " AD" v. all markers
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Marker NFams NAff Z-value Asy P Emp P Iters
---------- ------ ------ ---------- ------ ------ ------
D14S52 3 16 -0.2 0.5969 0.5142 500 APM-IBS .
D14S52 3 16 0.2 0.4336 0.3047 500 GPM-IBS .
D14S43 3 16 3.8 0.0001 0.0014 500 APM-IBS ***
D14S43 3 16 3.4 0.0003 0.0240 500 GPM-IBS **
D14S53 3 15 0.7 0.2507 0.1802 500 APM-IBS .
D14S53 3 15 2.8 0.0024 0.0115 500 GPM-IBS *
>> apm AD ibd
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APM for trait " AD" v. all markers
------------------------------------------------
NOTE: Identity-by-descent based statistic used.
Marker NFams NAff Z-value Asy P Emp P Iters
---------- ------ ------ ---------- ------ ------ ------
D14S52 3 30 0.7 0.2505 0.1960 500 APM-IBD .
D14S52 3 30 1.4 0.0834 0.1004 500 GPM-IBD +
D14S43 3 31 2.2 0.0138 0.0160 500 APM-IBD +
D14S43 3 31 3.1 0.0008 0.0100 500 GPM-IBD **
D14S53 3 30 0.8 0.2199 0.1863 500 APM-IBD .
D14S53 3 30 1.0 0.1559 0.0632 500 GPM-IBD +
>> set ple 1
>> apm AD
------------------------------------------------
APM for trait " AD" v. all markers
------------------------------------------------
----------- APM analysis for "D14S43" --------------
Overall statistics T NFam Asy-P InvZ-P
Aff-Aff
f(p) = 1 4.087 3 0.0000 0.0011
f(p) = 1/sqrt(p) 3.707 3 0.0001 0.0009
f(p) = 1/p 1.743 3 0.0406 0.0137
Aff-UnA
f(p) = 1 -1.184 2 0.1182 0.0991
f(p) = 1/sqrt(p) -1.734 2 0.0414 0.0627
f(p) = 1/p -1.345 2 0.0893 0.0279
Aff-Aff v. Aff-UnA
f(p) = 1 7.263 3 0.0000 0.0013
f(p) = 1/sqrt(p) 5.841 3 0.0000 0.0032
f(p) = 1/p 2.729 3 0.0032 0.0162
GPM
f(p) = 1 4.094 3 0.0000 0.0296
f(p) = 1/sqrt(p) 3.362 3 0.0004 0.0133
f(p) = 1/p 1.987 3 0.0235 0.0320
Total of 16 affecteds and 5 unaffecteds used.
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