Class | Analysis and data manipulation command |
Name | linkage |
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)
<< (qtlpair) | Up to index | >> (lod) |