Family-based association analysis
--tdt [{exact | exact-midp | poo}] ['perm' | 'mperm='<value>] ['perm-count'] [{parentdt1 | parentdt2 | pat | mat}] ['set-test']
Given case/control phenotypes and pedigree information, --tdt normally computes parenTDT (see the PLINK 1.07 documentation for details), transmission disequilibrium test, and combined test statistics, writing results to plink.tdt.
- A Mendel error check is performed before the main tests; offending genotypes are treated as missing by this analysis. --mendel-multigen extends this check in the usual way; however, --mendel-duos is not currently supported.
- By default, the basic TDT p-value is based on a chi-square test unless you request the exact binomial test with 'exact' or 'exact-midp'. (The parenTDT and combined tests are always based on chi-square stats for now since the corresponding exact tests are more complex, but we do know how to implement them; contact us if you want us to do so.)
- 'perm'/'mperm=<value>' requests a family-based adaptive or max(T) permutation test. 'perm-count' has the usual meaning. By default, the permutation test statistic is the basic TDT p-value; 'parentdt1'/'parentdt2' cause parenTDT or combined test p-values, respectively, to be considered instead.
- 'set-test' tests the significance of variant sets. This cannot be used with exact tests.
The 'poo' modifier causes a parent-of-origin analysis to be performed instead, with transmissions from heterozygous fathers and heterozygous mothers considered separately. Results are reported to plink.tdt.poo in this case.
- The parent-of-origin analysis does not currently support exact tests.
- By default, the permutation test statistic is the absolute parent-of-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT chi-square statistics, respectively, to be considered instead.
--dfam ['no-unrelateds'] ['perm' | 'mperm='<value>] ['perm-count'] ['set-test']
--dfam executes an extended version of the sib-TDT (see Spielman RS, Ewens WJ (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test) which includes clusters of unrelated individuals, writing results to plink.dfam.
- For backward compatibility, all missing-phenotype samples are treated as controls. You can use --prune to remove them from the analysis instead.
- If clusters are not defined via --within, all unrelated individuals are treated as belonging to the same cluster.
- --mendel-multigen, 'perm', 'mperm=<value>', 'perm-count', and 'set-test' have the usual effects.
- To remove unrelated individuals from the test (reducing it to the original sib-TDT), add the 'no-unrelateds' modifier.
--qfam ['perm' | 'mperm='<value>] ['perm-count'] ['emp-se']
--qfam-parents ['perm' | 'mperm='<value>] ['perm-count'] ['emp-se']
--qfam-between ['perm' | 'mperm='<value>] ['perm-count'] ['emp-se']
--qfam-total ['perm' | 'mperm='<value>] ['perm-count'] ['emp-se']
For family-based quantitative trait association analysis, PLINK offers the QFAM procedure, which combines a simple linear regression of phenotype on genotype with a special permutation test which corrects for family structure. Genotypes are divided into between-family and within-family components, the components are permuted separately, and then association analysis is performed on the within-family component (--qfam, --qfam-parents), between-family component (--qfam-between), or their sum (--qfam-total). Refer to the PLINK 1.07 documentation for a detailed discussion of the method.
- A Mendel error check is performed before the main tests; offending genotypes are treated as missing by this analysis. --mendel-multigen extends this check in the usual way; however, --mendel-duos is not currently supported.
- Permutation is required. 'perm' and 'perm-count' have the usual meanings. However, 'mperm=<value>' just specifies a fixed number of permutations; due to the way within-family genotype components are flipped, the method does not support a proper max(T) test.
- The output files are slightly different from PLINK 1.07 ('P' in header line has been renamed to 'RAW_P' to reduce likelihood of misinterpretation, and the .perm file doesn't have a 'STAT' field).
- The 'emp-se' modifier adds BETA and EMP_SE (empirical standard error for beta) fields to the .perm output file.
- Zero genotype variance now consistently yields 'NA' results.
- We've also made minor changes to how overlapping trios are handled, so NIND values may occasionally be different than PLINK 1.07's.
- Covariates are not currently supported.
--tucc ['write-bed']
--tucc generates a new dataset where, for each trio, a case sample is created with the child's genotypes, and a pseudo-control sample is created with all the untransmitted alleles.
- The new dataset only contains autosomal diploid variants.
- For backward compatibility, this flag defaults to writing plink.tucc.ped, with no accompanying .map file. This behavior is deprecated; add the 'write-bed' modifier to generate a complete binary fileset instead.
- When either parental genotype is missing, the corresponding case and pseudo-control genotypes are set to missing. This also happens for Mendel errors; --mendel-multigen extends the Mendel error check in the usual way.
Report postprocessing >>
|