The R extension for RTest is available HERE. For details on the format of this script please refer to the RTest method documentation.
We analyze association with a binary trait named X6 conditioning on 3 covariates X8, X9, X10. Group information is provided by race. For each testing group, data is first cleaned by removing samples missing greater than 50% calls, then by removing variants missing 50% calls.
The following command uses the default parameter settings in the R script:
vtools associate variant X6 --covariates X8 X9 X10 race \
-m "RTest ~/MetaSKAT.VAT.R --name MetaSKAT --out_type 'D' --group_colname 'race' " \
--discard_samples '%(NA)>0.5' --discard_variants '%(NA)>0.5' \
--group_by 'refGene.name2' -j8 --to_db MetaSKAT > MetaSKAT.txt
INFO: Loading R script '/home/gw/MetaSKAT.VAT.R'
INFO: 252 samples are found
INFO: 131 groups are found
INFO: Starting 8 processes to load genotypes
Loading genotypes: 100% [===================================] 252 72.5/s in 00:00:03
Testing for association: 100% [==============================] 131/122 10.4/s in 00:00:12
INFO: Association tests on 131 groups have completed. 122 failed.
INFO: Using annotation DB MetaSKAT in project mskat.
INFO: Annotation database used to record results of association tests. Created on Tue, 16 Apr 2013 01:40:03
INFO: 131 out of 23242 refgene.name2 are annotated through annotation database MetaSKAT
Note that with such stringent cleaning criteria only 9 out of 131 groups are analyzed. In the R program we throw an error on having no samples, only one variant, or only one study group. Please take a look at the *.log file for details of the errors.
refGene_name2 pvalue_MetaSKAT n_pop1_MetaSKAT n_pop2_MetaSKAT n_pop3_MetaSKAT
gene1 0.686969 79 84 NAN
gene2 0.0697923 84 68 NAN
gene3 0.0684316 81 83 NAN
gene4 0.426611 63 84 NAN
gene5 0.591128 70 77 NAN
gene6 0.00586012 84 81 NAN
gene7 0.306343 77 84 NAN
gene8 0.0951658 81 84 NAN
gene9 0.0988938 84 84 84
From the way MetaSKAT.VAT.R is written we known out_type and group_colname are required. They have to be explicitly specified at all times. Other parameters have default values, which can be altered by passing them like, for example:
... -m "RTest ~/MetaSKAT.VAT.R --name MetaSKAT \
--out_type 'D' --group_colname 'race' --pval.method 'davies' " ...