clumpingResult class

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Description

A result of procedure for snp clumping produced by clump_snps

Details

Always a named list of eleven elements

  1. X numeric matrix, consists of one snp representative for each clump

  2. y numeric vector, phenotype

  3. SNPnumber numeric vector, which columns in SNP matrix X_all are related to clumps representatives

  4. SNPclumps list of numeric vectors, which columns in SNP matrix X_all are related to clump members

  5. X_info data.frame, mapping information about SNPs from .map file. Copied from the result of screening procedure.

  6. selectedSnpsNumbers numeric vector, which rows of X_info matrix are related to selected clump representatives

  7. X_all numeric matrix, all the snps that passed screening procedure

  8. numberOfSnps numeric, total number of SNPs before screening procedure

  9. selectedSnpsNumbersScreening numeric vector, which rows of X_info data.frame are related to snps that passed screening

  10. pVals numeric vector, p-values from marginal tests for each snp

  11. pValMax numeric, p-value used in screening procedure

See Also

screeningResult clump_snps