selectionResult: selectionResult class

Description Details See Also

Description

A result of applying SLOPE to matrix of SNPs obtained by clumping produced. Result of function select_snps

Details

Always a named list of eighteen elements

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

  2. effects numeric vector, coefficients in linear model build on snps selected by SLOPE

  3. R2 numeric, value of R-squared in linear model build on snps selected by SLOPE

  4. selectedSNPs which columns in matrix X_all are related to snps selected by SLOPE

  5. y selectedClumps list of numeric vectors, which columns in SNP matrix X_all are related to clump members selected by SLOPE

  6. lambda numeric vector, lambda values used by SLOPE procedure

  7. y numeric vector, phenotype

  8. clumpRepresentatives numeric vector, which columns in SNP matrix X_all are related to clumps representatives

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

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

  11. X_clumps numeric matrix, consists of one snp representative for each clump

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

  13. selectedSnpsNumbers numeric vector, which rows of X_info data.frame are related to snps that were selected by SLOPE

  14. clumpingRepresentativesNumbers numeric vector, which rows of X_info data.frame are related to snps that are clump represenatives

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

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

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

  18. fdr numeric, false discovery rate used by SLOPE

See Also

screeningResult clumpingResult select_snps SLOPE


geneSLOPE documentation built on May 30, 2017, 1:22 a.m.