Sib-pair Command: tab


ClassAnalysis and data manipulation command
Nametab
Arguments [<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.

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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