![]() ![]() Note: Parameter expansion can be used when specifying phenotypes/covariates (e.g. To specify if header in transposed phenotype file only contains sample IID (assume FID=IID) BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES. Indexes of columns to ignore in transposed phenotype file QCTools (Quality Control Tools for Video Preservation) helps users analyze and. Index of phenotype name column in transposed phenotype file To use a phenotype file in transposed format (e.g. ![]() Use for each covariate you want to include in the analysisĬomma separated list of covariates to include in the analysisĬomma separated list of categorical covariates to include in the analysisĬomma separated list of covariates to ignoreįile containing predictions from Step 1 (see Overview). Use for each phenotype you want to include in the analysisĬomma separated list of phenotypes to include in the analysisĬomma separated list of phenotypes to ignore from the analysis Inclusion file that lists IDs of variants to keep regardless of minimum MAC filterĮxclusion file that lists IDs of variants to remove unless MAC is above threshold Inclusion file that lists IDs of variants to keepĮxclusion file that lists IDs of variants to remove Inclusion file that lists individuals to retain in the analysisĮxclusion file that lists individuals to remove from the analysis Specify to use the first allele as the reference allele for BGEN or PLINK bed/bim/fam file input Sample file corresponding to input BGEN file SourceForge ranks the best alternatives to icy.tools in 2022. file.bgen, or bed/bim/fam prefix that assumes file.bed, file.bim, file.fam exist, or pgen/pvar/psam prefix that assumes file.pgen, file.pvar, file.psam exist Compare icy.tools alternatives for your business or organization using the curated list below. One of the output files from these two commands is included in example/test_bin_out_firth_Y1.regenie. In Step 2, a set of imputed SNPs are tested for association using aįirth logistic regression model. In Step 1, the whole genome regression model is fit to the traits, andĪ set of genomic predictions are produced as output. A test run on a set of binary traits can be achieved by the The directory examples/ contains some small example files that are ![]()
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