Class | Analysis and data manipulation command |
Name | tab |
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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