pruneSNP {aSPU}

Prune SNPs (related to aSPUs, aSPUsPath, MTaSPUsSet)

Description

When correlation matirx have highly correlated SNPs, the performance of aSPUs, aSPUsPath and MTaSPUsSet are not very good. Do pruning using this function.

Usage

pruneSNP(corSNP, rup = 0.95, rdown = -0.95)

Arguments

corSNP

Correlation matirx of the SNPs to be tested; estimated from a reference panel (based on the same set of the reference alleles as used in calculating Z-scores).

rup

pruning criteria, erase one SNP when correlation between two SNPs are larger than this value.

rdown

pruning criteria, erase one SNP when correlation between two SNPs are smaller than this value.

Value

a list object pruned.corSNP and to.erase. pruned.corSNP is pruned correlation matrix. to.erase is SNP index to erase to get purned object. (i.e. corSNP[-to.erase, -to.erase] = pruned.corSNP )

Author(s)

Il Youp Kwak

See Also

aSPUs aSPUsPath MTaSPUsSet

Examples

data(kegg9)
## example analysis using aSPUM test.
g <- kegg9$gene.info[1,1]  #  SOAT1 
## Take snps mapped on gene "SOAT1" from the information of gene.info and snp.info. 
snps <- which( ( kegg9$snp.info[,2] == kegg9$gene.info[kegg9$gene.info[,1] == g, 2] ) &
                 (kegg9$snp.info[,3] > kegg9$gene.info[kegg9$gene.info[,1] == g, 3] ) &
                 (kegg9$snp.info[,3] < kegg9$gene.info[kegg9$gene.info[,1] == g, 4] )  )
## Take subsets
newP <- kegg9$nP[snps] ;
ldsub <- kegg9$ldmatrix[snps, snps];

prSNP <- pruneSNP(ldsub) 
newP <- newP[-prSNP$to.erase]
ldsub <- ldsub[-prSNP$to.erase, -prSNP$to.erase ]

## Get p-value for gene SOAT1. Read vignette for details.
out <- aSPUs(newP, corSNP=ldsub , pow=c(1:8, Inf), n.perm=100, Ps=TRUE)

out$Ts
# This is a vector of Test Statistics for SPUM and aSPUM tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are SPUs test statistics.
# The last element aSPUs is minimum of them, aSPUs statistic.

out$pvs
# This is a vector of p-values for SPUs and aSPUs tests.
# SPUs1 to SPUsInf corresponds with the option pow=c(1:8, Inf)
# They are p-values for corresponding SPUs tests.
# The last element is p-value of aSPUs test.