Sib-pair Command: linkage


ClassAnalysis and data manipulation command
Namelinkage
Arguments [<marker locus 1> [<marker locus 2>]]

Performs Elston and Keats sib pair linkage analysis for codominant markers. Default is adjacent pairs of markers (ie marker 1 with marker 2, marker 2 with marker 3...). If one marker is named, then gives estimate of recombination distance to all other markers.

Example:

>> include cavanaughex.in
>> linkage
---------------------------------------------------
Inter-marker sib pair linkage analysis
---------------------------------------------------

Marker 1       Marker 2       Sibships Sibpairs  r(IBD) Recomb
-------------- -------------- -------- --------  ------ -------
D16S769        D16S3145             55       68   0.590   0.116 0.074--0.180
D16S3145       D16S753              56       73   0.367   0.197 0.129--0.307
D16S753        D16S409              56       74   0.590   0.116 0.075--0.177
D16S409        D16S411              56       73   0.611   0.109 0.071--0.167
D16S411        D16S419              56       73   0.598   0.113 0.074--0.174
D16S419        D16S415              55       72   0.583   0.118 0.076--0.181
D16S415        D16S771              54       71   0.282   0.235 0.152--0.386

#
# It is not a particularly powerful or accurate approach:
#
>> sho map

User specified marker map:

Marker         Pos (cM)   Theta
-----------    --------   -----
D16S769           53.71   0.329   26066263 (chr 16)
D16S3145          55.01   0.013   26784604 (chr 16)
D16S753           60.12   0.049   31181005 (chr 16)
D16S409           61.00   0.009   47333369 (chr 16)
D16S411           62.23   0.012   48294236 (chr 16)
D16S419           67.69   0.052   51510863 (chr 16)
D16S415           69.15   0.014   52228236 (chr 16)
D16S771           70.85   0.017   53066505 (chr 16)


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