selectionResult: selectionResult class

In psobczyk/geneSLOPE: Genome-Wide Association Study with SLOPE

selectionResult class

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

psobczyk/geneSLOPE documentation built on July 5, 2025, 1:23 a.m.