A result of applying SLOPE to matrix of SNPs obtained by
clumping produced. Result of function select_snps
Always a named list of eighteen elements
X
numeric matrix, consists of one snp representative for each clump
selected by SLOPE
effects
numeric vector, coefficients in linear model build on
snps selected by SLOPE
R2
numeric, value of R-squared in linear model build on
snps selected by SLOPE
selectedSNPs
which columns in matrix X_all
are related to snps selected by SLOPE
y
selectedClumps list of numeric vectors, which columns in SNP matrix
X_all
are related to clump members selected by SLOPE
lambda
numeric vector, lambda values used by SLOPE procedure
y
numeric vector, phenotype
clumpRepresentatives
numeric vector, which columns in SNP matrix X_all
are related to clumps representatives
clumps
list of numeric vectors, which columns in SNP matrix
X_all
are related to clump members
X_info
data.frame, mapping information about SNPs from .map file.
Copied from the result of clumping procedure
X_clumps
numeric matrix, consists of one snp representative for each clump
X_all
numeric matrix, all the snps that passed screening procedure
selectedSnpsNumbers
numeric vector, which rows of X_info
data.frame are related to snps that were selected by SLOPE
clumpingRepresentativesNumbers
numeric vector, which rows of X_info
data.frame are related to snps that are clump represenatives
screenedSNPsNumbers
numeric vector, which rows of X_info
data.frame are related to snps that passed screening
numberOfSnps
numeric, total number of SNPs before screening procedure
pValMax
numeric, p-value used in screening procedure
fdr
numeric, false discovery rate used by SLOPE
screeningResult
clumpingResult
select_snps
SLOPE
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