Sib-pair Command: tab


ClassAnalysis and data manipulation command
Nametab
Arguments[showmiss] [polychoric] [sampleweight <trait>] [<trait 1>...[<trait N>] | (ped <trait>)]

Print contingency table for one, two or N traits, along with contingency chi-squares, Kruskal-Wallis test or odds ratio if appropriate. For RxC contingency tables where the second variable is a diallelic marker locus, allele frequencies and exact P-values testing Hardy-Weinberg Equilibrium are printed for each level of the first trait.

The default behaviour is to print a one-way table for each active variable. With the plevel at zero, this is a one line table laid out horizontally, but with higher verbosity levels, a full tabulation laid out row by row is printed.

If the showmiss keyword is present, then an additional level indicating that the trait value is missing is included in the table.

The polychoric option will calculate the polychoric correlation for a two-way table.

One can specify for a oneway table for a variable to be printed for each pedigree using the pedigree option, which is supplemented by the Tarone score test for extrabinomial variation if the trait is binary.

Example:

>> include linclex.in
>> tab 

lincl                x:     0       y:    16       n:    56
oneperfam            x:     0       y:    12       n:    60
D13S162              x:     6       y:    66 (11 unique values   1/4  ...6/8)
D13S160              x:     6       y:    66 (13 unique values   1/1  ...5/6)
D13S170              x:    14       y:    58 (25 unique values   1/3  ...10/10)

>> tab lincl D13S162


------------------------------------------------
Cross-tabulation of "lincl" ... "D13S162"
------------------------------------------------
  lincl     D13S162      Count  Percent
----------------------------------------
     n         1/4          3      4.5
     n         1/7          1      1.5
     n         2/4          7     10.6
     n         2/5          1      1.5
     n         3/4          3      4.5
     n         4/4          8     12.1
     n         4/5          7     10.6
     n         4/6          4      6.1
     n         4/7          8     12.1
     n         4/8          6      9.1
     n         6/8          2      3.0
     y         2/4          1      1.5
     y         4/4         14     21.2
     y         4/7          1      1.5
----------------------------------------
  Total                    66 (and  6  missing)

>> tab D13S162 lincl

------------------------------------------------
Cross-tabulation of "D13S162" ... "lincl"
------------------------------------------------

                      lincl
D13S162            n            y      Odds Ratio (95%CI)
           ----------------------------------------------------
    1/4         3 (1.00)     0 (.000)      1.00
    1/7         1 (1.00)     0 (.000)      2.33 (0.03--182.92)
    2/4         7 (.875)     1 (.125)      1.40 (0.04--43.79)
    2/5         1 (1.00)     0 (.000)      2.33 (0.03--182.92)
    3/4         3 (1.00)     0 (.000)      1.00 (0.02--66.07)
    4/4         8 (.364)    14 (.636)     11.94 (0.55--260.30)
    4/5         7 (1.00)     0 (.000)      0.47 (0.01--28.73)
    4/6         4 (1.00)     0 (.000)      0.78 (0.01--49.91)
    4/7         8 (.889)     1 (.111)      1.24 (0.04--38.30)
    4/8         6 (1.00)     0 (.000)      0.54 (0.01--33.47)
    6/8         2 (1.00)     0 (.000)      1.40 (0.02--97.44)
           ----------------------------------------------------
     Total     50 [.758]    16 [.242]

    No. complete observations =    66
    LR contingency chi-square =  31.96
           Degrees of freedom =  10
           Asymptotic P-value =   0.0004
              Empiric P-value =   0.0020 (132000 MCMC iterations)
             Trend chi-square =   0.61   (P=0.4365)


>> tab ped lincl
Pedigree versus "lincl":

Pedigree    Affected (Prop)   Total   Missing
---------- ---------------- --------  -------
1               2 (0.2857)         7        0
2               2 (0.2222)         9        0
3               2 (0.1818)        11        0
4               1 (0.2500)         4        0
5               0 (0.0000)         5        0
6               1 (0.2500)         4        0
7               0 (0.0000)         4        0
8               1 (0.2000)         5        0
9               1 (0.2500)         4        0
10              1 (0.2500)         4        0
11              1 (0.2500)         4        0
12              1 (0.3333)         3        0
13              2 (0.5000)         4        0
14              1 (0.2500)         4        0

   Number of pedigrees = 14
   Number of affecteds = 16
       Number observed = 72
   Proportion affected = 0.2222
  Variance Chi-square  =        4.96 (df=  13, P=0.9761)
    Tarone Score Test  =        3.38 (P=0.0661)
Intraclass correlation =       -0.1522

>> count lincl

Count where "lincl":

Pedigree        Con=T    Num   ASPs   Trios    4+
-------------- ------ ------- ------ ------ ------
1                   2       7      1      0      0
2                   2       9      1      0      0
3                   2      11      0      0      0
4                   1       4      0      0      0
6                   1       4      0      0      0
8                   1       5      0      0      0
9                   1       4      0      0      0
10                  1       4      0      0      0
11                  1       4      0      0      0
12                  1       3      0      0      0
13                  2       4      1      0      0
14                  1       4      0      0      0
         Total     16      72      3      0      0


Number of matched persons   =16 out of 72 (22.2%)
Number of matched pedigrees =12 out of 14 (85.7%)


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