clumpingResult {geneSLOPE} | R Documentation |
clumpingResult class
Description
A result of procedure for snp clumping produced by clump_snps
Details
Always a named list of eleven elements
-
X
numeric matrix, consists of one snp representative for each clump -
y
numeric vector, phenotype -
SNPnumber
numeric vector, which columns in SNP matrixX_all
are related to clumps representatives -
SNPclumps
list of numeric vectors, which columns in SNP matrixX_all
are related to clump members -
X_info
data.frame, mapping information about SNPs from .map file. Copied from the result of screening procedure. -
selectedSnpsNumbers
numeric vector, which rows ofX_info
matrix are related to selected clump representatives -
X_all
numeric matrix, all the snps that passed screening procedure -
numberOfSnps
numeric, total number of SNPs before screening procedure -
selectedSnpsNumbersScreening
numeric vector, which rows ofX_info
data.frame are related to snps that passed screening -
pVals
numeric vector, p-values from marginal tests for each snp -
pValMax
numeric, p-value used in screening procedure