Sib-pair Command: clumpld

Class	Analysis and data manipulation command
Name	clumpld
Arguments	[<critical_P_value> [<critical_LD_r_value> [<map_window_width>]]] nosave

Prunes single locus association test results based on the LD with more significant markers. The optional parameters are the genome-wide critical P-value (defaults to α=0.05); the maximum allowable LD r for retention of a less signficant neighbour of the current iterated ("peak") marker (defaults to r=0.5); and the maximum map interval to evaluate less signficant neighbours of the current iterated ("peak") marker (defaults to 1 cM/Mbp). Results are saved (if nosave modifier is absent) as the test statistic for each marker: 0="outside critical α", 1="redundant marker", 2="retained".

To duplicate the results from PLINK, need:

clump 1e-4 0.707 2.5

>> ass modzt
>> summary

Test: "ass modzt".

Total number of tests = 6

Locus              Chr  Position  P-value   -log10(P)   FDR
------------------ --- ---------- -------  ---------- -------
rs74485684         11  30.242287  3e-14       13.487  2e-13   P=2.5e-17     1.9e-07
rs4071559          11  30.344725  6e-14       13.205  1e-13   30344725 (chr 11) C/T
rs1782507          11  30.243868  1e-11       10.831  1e-11   [T/G] PR (ORIG 11:30243868:G:T)
rs17293443         15  67.437863  6e-11       10.196  3e-11   [T/C] PR (ORIG 15:67437863:C:T)
15:67437863        15  67.437863  6e-10        9.225  1e-10   P=3.2e-09     2.5e-02

>> set ple 2

NOTE:  Print level  2

>> clumpld

------------------------------------------------------
LD Clumping for "ass modzt"
------------------------------------------------------
Critical alpha   = 0.0500
Eligible markers = 6
LD r threshold   = 0.5000
Testing window   =     1.000000

Dropped Marker  Chr  Position   Stat            Neighbour        r
--------------- --- ----------- ------------ ----------------------
rs4071559       11    30.344725 0.623426E-13 rs74485684      0.9971
15:67437863     15    67.437863 0.596245E-09 rs17293443      0.9926

Can drop 2 of 6 eligible markers.

Selected Marker Chr  Position   Stat
--------------- --- ----------- ------------
rs74485684      11    30.242287 0.325914E-13
rs1782507       11    30.243868 0.147700E-10
rs17293443      15    67.437863 0.636504E-10
rs12445547      16    88.518569 0.336986E-07

>> summary tab                                                                

Test: "LD pruning: 0=Below_cut 1=Superfluous 2=Keep" (takes 2 distinct values).

Category     Count Percent
---------- ------- -------
1=Superflu       2    33.3
2=Keep           4    66.7

See also:

dis	intragametic association