Sib-pair Command: set nhap


ClassGlobal
Nameset nhap
Arguments <maximum_number_of_haplotypes>

Sib-pair implements two approaches to haplotyping: a full maximum likelihood log-linear model, or simple tabulation of haplotypes imputed from parent-offspring transmissions. The former algorithm can be used for samples of unrelated individuals, but doesn't work well when there are many haplotypes, while the latter requires informative families. The first algorithm is the default, unless there are more than maxhap possible haplotypes for the given system is encountered. The value of maxhap is set by this command, and defaults to 100.

Example:

>> include cavanaughex.in
>> keep D16S769 D16S3145
>> fre snp
Marker         NAll  Allele(s)    Freq   Het    Ntyped
-------------- ---- -----------   ------ ------ ------
D16S769           7     1..   8    -     0.7342    204 26066263 (chr 16)
D16S3145          9     1..   9    -     0.6377    215 26784604 (chr 16)

>> dis D16S769 D16S3145
---------------------------------------------------
Inter-marker allelic association analysis
---------------------------------------------------

Marker 1       Marker 2            N mean D'    r2 Chi-sq  df  asy P
-------------- -------------- ------ ------- ----- ------ --- ------
NOTE : Identifiability problem in variance-covariance matrix for betas.
...
D16S769        D16S3145         88   0.172  -      37.0  48 0.8756 LD  .

>> set nhap 20
>> dis D16S769 D16S3145
Marker 1       Marker 2            N mean D'    r2 Chi-sq  df  asy P
-------------- -------------- ------ ------- ----- ------ --- ------
D16S769        D16S3145          140   0.165  -      32.1   48 0.6802 LD  .


<< (set hre)Up to index>> (set map)