The 1xc table tests

The 1xc table tests

the_1xc_table_tests(n, pi0, chacko.test = FALSE)

Arguments

n

the observed counts (a 1xc vector, where c is the number of categories)

pi0

given probabilities (a 1xc vector)

chacko.test

if TRUE, only performs the Chacko test

Value

NULL. This function should be called for its printed output

Examples

# Genotype counts for SNP rs 6498169 in RA patients
the_1xc_table_tests(n = snp6498169$complete$n, pi0 = snp6498169$complete$pi0)
#> Estimate of pi_1: 276 / 774 = 0.357 (pi_1,0 = 0.402) 
#> Estimate of pi_2: 380 / 774 = 0.491 (pi_2,0 = 0.479) 
#> Estimate of pi_3: 118 / 774 = 0.152 (pi_3,0 = 0.119) 
#> Method                 P-value  (test statistic) 
#> --------------------------------------------------- 
#> Pearson chi-squared    0.0032   (T = 11.481, df = 2) 
#> Likelihood ratio       0.0040   (T = 11.038, df = 2) 
#> --------------------------------------------------- 
# subset of 10 patients
the_1xc_table_tests(n = snp6498169$subset$n, pi0 = snp6498169$subset$pi0)
#> Estimate of pi_1:  6 / 10 = 0.600 (pi_1,0 = 0.402) 
#> Estimate of pi_2:  1 / 10 = 0.100 (pi_2,0 = 0.479) 
#> Estimate of pi_3:  3 / 10 = 0.300 (pi_3,0 = 0.119) 
#> Method                 P-value  (test statistic) 
#> --------------------------------------------------- 
#> Pearson chi-squared    0.0346   (T = 6.727, df = 2) 
#> Likelihood ratio       0.0270   (T = 7.221, df = 2) 
#> Exact multinomial      0.0479
#>  
#> Mid-P multinomial      0.0465
#>  
#> --------------------------------------------------- 
# Example for the Chacko test: Hypothetical experiment
the_1xc_table_tests(n = hypothetical, pi0 = c(0.402, 0.479, 0.119), TRUE)
#> The Chacko test: P = 0.002168, T = 12.268 (df = 2)