This is the input format for the GSMR analysis. Note: the two steps above guarantee that the LD correlations are calculated based on the effect alleles for the SNP effects. Note: all the analyses implemented in this R-package only require the summary data e. This is an optional process. See also --pfilter below. Or, going in the other direction, the ' intercept ' modifier lets you also see the intercept-column fit. Firth regression can be slow.
To trade off some accuracy for speed, you can use the ' firth-residualize ' modifier, which implements the shortcut described in Mbatchou J et al.
This shortcut must be used with 'hide-covar', and disables some other --glm features. It is not recommended if you have a significant number of missing genotypes, or if you have any other reason to expect covariate betas to change in a relevant way between variants. Since running --glm without at least e. This modifier did not exist, and the corresponding check was not performed, before 28 Mar The ' log10 ' modifier causes p-values to be reported in -log10 p form. Refer to the file format entry for a list of supported column sets.
A multicollinearity check is performed before each regression. When it fails, the regression is skipped and 'NA' results are reported. The main part of this check is a variance inflation factor calculation. If that value is larger than 50 , the check fails.
You can change the upper bound with --vif. Correlations between predictors are also checked; if any correlation is larger than 0. You can change this upper bound with --max-corr. This column distinguishes some other error types, too. The following error codes are currently reported: '. This usually means that all alleles are constant. Meaning was different before 20 Mar Note that, in 'genotypic' mode, this happens for every biallelic variant with no homozygous-minor genotypes, since the additive and dominance-deviation columns are identical in that case.
Those variants must be analyzed without 'genotypic'. The result is still reported in this case, but it's less accurate than usual. The VIF check is known to be overly strict in several common scenarios; in particular, categorical covariates with a large number of categories will set it off. Do not be afraid to greatly increase the --vif threshold after you have studied the problem and confirmed that moderate multicollinearity does not interfere with your analysis.
Covariates are also checked before any variants are processed. This includes a covariate-only version of the multicollinearity check described above, along with a covariate-scale check which identifies scenarios where --covar-variance-standardize can be expected to help a lot. By default, if this check fails, PLINK 2 errors out; to just skip the affected regressions instead, add the ' skip-invalid-pheno ' modifier.
Malformed input error messages now include line numbers. Basic parent-of-origin test implemented. Basic --score implemention. Markers with identical bp coordinates no longer cause 1. D-prime computations "--r2 dprime", --ld, --blocks, --clump involving variants on the X chromosome now appropriately downweight males relative to females.
We hope we were the only actual victims of this. VCF allele code Nazi now just issues a warning, since some pipelines actually depend on violating the official spec. VCF 'N' reference allele now handled in a saner manner converted to and back from missing. VCF generator now forces the A2 reference allele to always be known, and outputs '. LD-based result clumping --clump is now supported. This multithread efficiency issue will be solved in the near future. Also see the major bugfix above.
Optional 'chr' chromosome prefixes may now be partly or entirely capitalized. Gzipped and binary Oxford genotype files can now be directly imported. Fixed contig name handling bug which slipped into 23 Jan builds. Hardy-Weinberg and Fisher's exact tests now support mid-p adjustments. Proper handling of ambiguous sex codes.
Y chromosome "nonmissing nonmale genotypes" warning no longer gets sexes backwards oops. Mitochondrial DNA no longer required to be haploid though there are no plans to support full polyploidy. Cluster permutation and --covar-name range handling bugfixes. Basic --test-missing. Fixed a bug which sometimes came up when using --ibs-test or association analysis commands while filtering out samples.
Also fixed the --distance segfault introduced in the 18 Dec build; sorry about that. PRSice will automatically substitute with If the files are chr1. Chromosome number substitution will not be performed on the external fam file as the fam file should be the same for all chromosomes. In theory, we can support BGEN v1.
As BGEN does not store the phenotype information and sometime not even the sample ID, you must provide a phenotype file --pheno. Alternatively, if you have a sample file containing the phenotype information, you can provide it with. The sample file is required even if --no-regress is set as the sample ID is required for output.
This requirement might be losen in future versions. But hard-thresholding can be performed by using the --hard option. SNPs will then coded as the genotype 0,1 or 2 and filtered according to threshold set by --hard-thres. If no such genotype is presented, the SNP will be coded as missing. See here for more detail. To speed up the clumping process, you can allow PRSice to generate a large intermediate file, containing the hard coded genotypes in PLINK binary format by using the --allow-inter option.
An external phenotype file can be provided to PRSice using the --pheno parameter. The rest of the columns can be the phenotype s. To specify a trait within the phenotype file, the column name for the trait can be specified using --pheno-col , providing that the phenotype file contains a header. Multiple column name can be provided via a comma separated list: e.
Trait s not found within the phenotype file will be automatically skipped. When the target sample is small e. The LD reference follows the same notion as the target dataset. When a LD reference file is not provided and --no-clump is not specified, the target file will be used as the LD reference panel.
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