Class | Global |
Name | list | ls |
Arguments | [<loc1> [[to] <locN> [$(a|q|m|h|x|A|D)[m|r]] |
List of loci in current analysis. The "$<letter>" keyword denotes the list of of one class of locus, which can be reordered according to genetic map position (m) or in reverse (r) to the dataset ordering (mr is by reverse map order). The modifiers do not affect A and D, which are the sets of all active and all inactive loci respectively.
$a | All active binary traits |
$ar | All active binary traits in reverse dataset order |
$q | All active quantitative traits |
$qr | All active quantitative traits in reverse dataset order |
$m | All active codominant markers |
$mr | All active codominant markers in reverse dataset order |
$mm | All active codominant markers in map order |
$mmr | All active codominant markers in reverse map order |
$x | All active X-chromosomal markers |
$xr | All active X-chromosomal markers in reverse dataset order |
$xm | All active X-chromosomal markers in map order |
$xmr | All active X-chromosomal markers in reverse map order |
$h | All active haploid markers (Y or mitochondrial) |
$hr | All active haploid markers in reverse dataset order |
$hm | All active haploid markers in map order |
$hmr | All active haploid markers in reverse map order |
$A | All active loci |
$D | All dropped loci |
Loci can be referred to by their index in the list of loci (1..N).
Using list gives a full output with one line per locus, while ls gives an abbreviated output mimicking the results of the unix ls -F command.
Example:
>> include williamsex.in >> lis Locus Type Position --------------- ---- ---------------- age q 6 CHD a 7 carrier a 8 adjChol q 9 ldl m 10-- 11 Number of marker loci= 1 Bonferroni corr. 5% = 0.050000 Bonferroni corr. 1% = 0.010000 Bonferroni corr. 0.1%= 0.001000 >> ls age* CHD* carrier* adjChol* ldl 4 active traits; 1 active markers. >> ls $q age* adjChol* 2 active traits; 0 active markers. >> ls $qr adjChol* age* 2 active traits; 0 active markers. >> ls 1 2 age* CHD* 2 active traits; 0 active markers. >> ls carrier -- ldl carrier* adjChol* ldl 2 active traits; 1 active markers.
See also:
show loci | locus information |
which | list positions of loci |
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