clumpingResult: clumpingResult class

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

clumpingResult class

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

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