RBT test

vtools show test RBT

Name:          RBT
Description:   Replication Based Test for protective and deleterious variants,
               Ionita-Laza et al 2011
usage: vtools associate --method RBT [-h] [--name NAME] [-q1 MAFUPPER]
                                     [-q2 MAFLOWER] [--alternative TAILED]
                                     [-p N] [--adaptive C]
                                     [--moi {additive,dominant,recessive}]

Replication Based Test for protective and deleterious variants, Ionita-Laza et
al 2011. Variant sites are scored based on -log transformation of probability
of having more than observed variants in cases/ctrls; the RBT statistic is
defined as sum of the variant sites scores. One-sided RBT is implemented in
addition to the two-sided statistic described in the RBT paper. p-value is
estimated via permutation test.

optional arguments:
  -h, --help            show this help message and exit
  --name NAME           Name of the test that will be appended to names of
                        output fields, usually used to differentiate output of
                        different tests, or the same test with different
                        parameters.
  -q1 MAFUPPER, --mafupper MAFUPPER
                        Minor allele frequency upper limit. All variants
                        having sample MAF<=m1 will be included in analysis.
                        Default set to 0.01
  -q2 MAFLOWER, --maflower MAFLOWER
                        Minor allele frequency lower limit. All variants
                        having sample MAF>m2 will be included in analysis.
                        Default set to 0.0
  --alternative TAILED  Alternative hypothesis is one-sided ("1") or two-sided
                        ("2"). Default set to 1
  -p N, --permutations N
                        Number of permutations
  --adaptive C          Adaptive permutation using Edwin Wilson 95 percent
                        confidence interval for binomial distribution. The
                        program will compute a p-value every 1000 permutations
                        and compare the lower bound of the 95 percent CI of
                        p-value against "C", and quit permutations with the
                        p-value if it is larger than "C". It is recommended to
                        specify a "C" that is slightly larger than the
                        significance level for the study. To disable the
                        adaptive procedure, set C=1. Default is C=0.1
  --moi {additive,dominant,recessive}
                        Mode of inheritance. Will code genotypes as 0/1/2/NA
                        for additive mode, 0/1/NA for dominant or recessive
                        model. Default set to additive

vtools associate rare status -m "RBT --name RBT -p 5000" --group_by name2 --to_db rbt -j8 >\
 rbt.txt

INFO: 3180 samples are found
INFO: 2632 groups are found
INFO: Starting 8 processes to load genotypes
Loading genotypes: 100% [===========================] 3,180 34.0/s in 00:01:33
Testing for association: 100% [===================================] 2,632/591 14.3/s in 00:03:03
INFO: Association tests on 2632 groups have completed. 591 failed.
INFO: Using annotation DB rbt in project test.
INFO: Annotation database used to record results of association tests. Created on Wed, 30 Jan 2013 05:32:45




vtools show fields | grep RBT

rbt.sample_size_RBT          sample size
rbt.num_variants_RBT         number of variants in each group (adjusted for specified MAF
rbt.total_mac_RBT            total minor allele counts in a group (adjusted for MOI)
rbt.statistic_RBT            test statistic.
rbt.pvalue_RBT               p-value
rbt.std_error_RBT            Empirical estimate of the standard deviation of statistic
rbt.num_permutations_RBT     number of permutations at which p-value is evaluated




head rbt.txt

name2   sample_size_RBT num_variants_RBT        total_mac_RBT   statistic_RBT   pvalue_RBT      std_error_RBT   num_permutations_RBT
AADACL4 3180    5       138     1.37261 0.898102        2.99763 1000
ABCB6   3180    7       151     4.94419 0.665335        3.29949 1000
ABCG5   3180    6       87      5.1935  0.413586        2.98032 1000
ABCG8   3180    12      152     4.96566 0.769231        4.03695 1000
ABL2    3180    4       41      2.67589 0.456543        2.29237 1000
ACADL   3180    5       65      2.18841 0.696304        2.64459 1000
ACADM   3180    4       103     2.04935 0.678322        2.58183 1000
ACAP3   3180    3       17      2.32431 0.422577        1.95933 1000
ABCD3   3180    3       42      1.10394 0.797203        2.16152 1000